Serialized Form (Fiji Javadocs 0-SNAPSHOT API)

Package <Unnamed>

Class BorderPanel extends Panel implements Serializable
- Serialized Fields
  - label
```
String label
```

Class Color_Inspector_3D.Menu extends JMenuBar implements Serializable

Serialized Fields

stringColor
```
String stringColor
```
stringText
```
String stringText
```
stringAxes
```
String stringAxes
```
stringRotation
```
String stringRotation
```
stringResetManip
```
String stringResetManip
```
stringFitImage
```
String stringFitImage
```
stringEnglish
```
String stringEnglish
```
stringManual
```
String stringManual
```
stringError1
```
String stringError1
```
stringOpen
```
String stringOpen
```
stringSaveVisualisation
```
String stringSaveVisualisation
```
stringSaveModified
```
String stringSaveModified
```
stringDuplicateVisualisation
```
String stringDuplicateVisualisation
```
stringDuplicateModified
```
String stringDuplicateModified
```
stringQuit
```
String stringQuit
```
stringGradient
```
String stringGradient
```
stringComic
```
String stringComic
```
stringStart
```
String stringStart
```
stringphoto
```
String stringphoto
```
stringCG
```
String stringCG
```
stringPalette
```
String stringPalette
```
stringWebColors
```
String stringWebColors
```
stringColorCube1
```
String stringColorCube1
```
stringColorCube2
```
String stringColorCube2
```
stringSeg1
```
String stringSeg1
```
stringSeg2
```
String stringSeg2
```
stringSeg3
```
String stringSeg3
```
stringSeg4
```
String stringSeg4
```
stringSeg5
```
String stringSeg5
```
stringSeg6
```
String stringSeg6
```

Class DisplayChangeEvent extends EventObject implements Serializable
- Serialized Fields
  - type
```
int type
```
  - value
```
int value
```

Class HybridDateFormat extends DateFormat implements Serializable

serialVersionUID:: 4774881970558875024L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException

Throws:: IOException; ClassNotFoundException

Serialized Fields

formatData
```
DateFormatSymbols formatData
```
defaultCenturyStart
```
Date defaultCenturyStart
```
pattern
```
String pattern
```
serialVersionOnStream
```
int serialVersionOnStream
```

Class IntField extends TextField implements Serializable
- Serialized Fields
  - value
```
int value
```
  - minValue
```
int minValue
```
  - maxValue
```
int maxValue
```
  - actionCommand
```
String actionCommand
```
Class IntSlider extends Panel implements Serializable
- Serialized Fields
  - bar
```
Scrollbar bar
```
  - field
```
IntField field
```
  - value
```
int value
```
  - minValue
```
int minValue
```
  - maxValue
```
int maxValue
```
  - actionCommand
```
String actionCommand
```

Class Manual_Tracking extends ij.plugin.frame.PlugInFrame implements Serializable

Serialized Fields

calxy
```
double calxy
```
calz
```
double calz
```
calt
```
double calt
```
cent
```
int cent
```
dotsize
```
int dotsize
```
linewidth
```
double linewidth
```
fontsize
```
int fontsize
```
col
```
Color[] col
```
i
```
int i
```
j
```
int j
```
k
```
int k
```
l
```
int l
```
m
```
int m
```
n
```
int n
```
txt
```
String txt
```
bold
```
Font bold
```
panel
```
Panel panel
```
butAdd
```
Button butAdd
```
butDlp
```
Button butDlp
```
butEnd
```
Button butEnd
```
butDel
```
Button butDel
```
trackdel
```
Choice trackdel
```
butDelAll
```
Button butDelAll
```
checkPath
```
Checkbox checkPath
```
choicecent
```
Choice choicecent
```
checkCent
```
Checkbox checkCent
```
labelCorr
```
Label labelCorr
```
butAddRef
```
Button butAddRef
```
butDelRef
```
Button butDelRef
```
titleRef
```
Label titleRef
```
checkShowRef
```
Checkbox checkShowRef
```
checkRef
```
Checkbox checkRef
```
butOvd
```
Button butOvd
```
butOvl
```
Button butOvl
```
butOvdl
```
Button butOvdl
```
butOverdots
```
Button butOverdots
```
butOverlines
```
Button butOverlines
```
butOverboth
```
Button butOverboth
```
checkText
```
Checkbox checkText
```
butLoad
```
Button butLoad
```
checkParam
```
Checkbox checkParam
```
butRetrieveZ
```
Button butRetrieveZ
```
labelEmpty1
```
Label labelEmpty1
```
labelEmpty2
```
Label labelEmpty2
```
labelEmpty3
```
Label labelEmpty3
```
labelEmpty4
```
Label labelEmpty4
```
labelParam
```
Label labelParam
```
labelEmpty5
```
Label labelEmpty5
```
labelTime
```
Label labelTime
```
caltfield
```
TextField caltfield
```
choicecalt
```
Choice choicecalt
```
labelxy
```
Label labelxy
```
calxyfield
```
TextField calxyfield
```
choicecalxy
```
Choice choicecalxy
```
labelz
```
Label labelz
```
calzfield
```
TextField calzfield
```
labelEmpty6
```
Label labelEmpty6
```
labelCent
```
Label labelCent
```
labelPix
```
Label labelPix
```
centsize
```
TextField centsize
```
labelDot
```
Label labelDot
```
dotsizefield
```
TextField dotsizefield
```
labelEmpty7
```
Label labelEmpty7
```
labelLine
```
Label labelLine
```
linewidthfield
```
TextField linewidthfield
```
labelEmpty8
```
Label labelEmpty8
```
labelFont
```
Label labelFont
```
fontsizefield
```
TextField fontsizefield
```
labelEmpty9
```
Label labelEmpty9
```
img
```
ij.ImagePlus img
```
imgtitle
```
String imgtitle
```
Width
```
int Width
```
Height
```
int Height
```
Depth
```
int Depth
```
Slice
```
int Slice
```
SliceTitle
```
String SliceTitle
```
canvas
```
ImageCanvas canvas
```
ip
```
ij.ImagePlus ip
```
stack
```
ij.ImageStack stack
```
win
```
ImageWindow win
```
sc
```
ij.process.StackConverter sc
```
dp
```
ij.plugin.filter.Duplicater dp
```
islistening
```
boolean islistening
```
xRoi
```
int[] xRoi
```
yRoi
```
int[] yRoi
```
roi
```
Roi roi
```
Nbtrack
```
int Nbtrack
```
NbPoint
```
int NbPoint
```
ox
```
int ox
```
oy
```
int oy
```
PixVal
```
int PixVal
```
prevx
```
int prevx
```
prevy
```
int prevy
```
Distance
```
double Distance
```
Velocity
```
double Velocity
```
pprevx
```
int pprevx
```
pprevy
```
int pprevy
```
trackZ
```
boolean trackZ
```
commentCorr
```
String commentCorr
```
islisteningRef
```
boolean islisteningRef
```
RefSet
```
boolean RefSet
```
DirIndex
```
int DirIndex
```
refx
```
int refx
```
refy
```
int refy
```
roiRef
```
Roi roiRef
```
gd
```
GenericDialog gd
```
gd1
```
GenericDialog gd1
```
gd2
```
GenericDialog gd2
```
VRMLgd
```
GenericDialog VRMLgd
```
od
```
ij.io.OpenDialog od
```
sd
```
ij.io.SaveDialog sd
```
FileName
```
String FileName
```
File
```
String File
```
dir
```
String dir
```
rt
```
ij.measure.ResultsTable rt
```
rtmp
```
ij.measure.ResultsTable rtmp
```
head
```
String[] head
```
rt3D
```
ij.measure.ResultsTable rt3D
```
in
```
BufferedReader in
```
line
```
String line
```
Token
```
StringTokenizer Token
```
CentringArray
```
String[] CentringArray
```
Centring
```
int Centring
```
sglBoxx
```
int sglBoxx
```
sglBoxy
```
int sglBoxy
```
sglBoxz
```
int sglBoxz
```
bkgdBoxx
```
int bkgdBoxx
```
bkgdBoxy
```
int bkgdBoxy
```
bkgdBoxz
```
int bkgdBoxz
```
QuantificationArray
```
String[] QuantificationArray
```
Quantification
```
int Quantification
```
DoQuantification
```
boolean DoQuantification
```
DoBleachCorr
```
boolean DoBleachCorr
```
DoVRML
```
boolean DoVRML
```
tmpx
```
int tmpx
```
tmpy
```
int tmpy
```
tmpz
```
int tmpz
```
tmpttl
```
int tmpttl
```
tmppixval
```
int tmppixval
```
limsx1
```
int limsx1
```
limsx2
```
int limsx2
```
limsy1
```
int limsy1
```
limsy2
```
int limsy2
```
limsz1
```
int limsz1
```
limsz2
```
int limsz2
```
sizeSgl
```
double sizeSgl
```
limbx1
```
int limbx1
```
limbx2
```
int limbx2
```
limby1
```
int limby1
```
limby2
```
int limby2
```
limbz1
```
int limbz1
```
limbz2
```
int limbz2
```
sizeBkgd
```
double sizeBkgd
```
Qsgl
```
double Qsgl
```
Qbkgd
```
double Qbkgd
```
Qttl
```
double Qttl
```
Qttl0
```
double Qttl0
```
QSglBkgdCorr
```
double QSglBkgdCorr
```
QSglBkgdBleachCorr
```
double QSglBkgdBleachCorr
```
StaticArray
```
String[] StaticArray
```
DynamicArray
```
String[] DynamicArray
```
Static
```
String Static
```
Dynamic
```
String Dynamic
```
StaticView
```
boolean StaticView
```
StaticViewObj
```
boolean StaticViewObj
```
StaticViewTraj
```
boolean StaticViewTraj
```
DynamicView
```
boolean DynamicView
```
DynamicViewStaticTraj
```
boolean DynamicViewStaticTraj
```
DynamicViewDynamicTraj
```
boolean DynamicViewDynamicTraj
```
dirVRMLstat
```
String dirVRMLstat
```
oswStat
```
OutputStreamWriter oswStat
```
dirVRMLdynam
```
String dirVRMLdynam
```
oswDynam
```
OutputStreamWriter oswDynam
```
vrmlCol
```
String[] vrmlCol
```
x
```
int x
```
y
```
int y
```
z
```
int z
```
xOld
```
int xOld
```
yOld
```
int yOld
```
zOld
```
int zOld
```
VRMLarray
```
int[][] VRMLarray
```
vrmlCount
```
int vrmlCount
```
DistOfView
```
double DistOfView
```
minTime
```
double minTime
```
maxTime
```
double maxTime
```
countBefore
```
int countBefore
```
countAfter
```
int countAfter
```
countTtl
```
int countTtl
```
key
```
String key
```
Tag
```
int Tag
```
TagOld
```
int TagOld
```
point
```
String point
```
pointNb
```
int pointNb
```
pointKey
```
String pointKey
```
lastPoint
```
String lastPoint
```
adapter
```
ImageAdapter adapter
```

Class OpenImage5DWindow extends Image5DWindow implements Serializable
- Serialized Fields
  - i5d
```
Image5D i5d
```
  - displayChangeListener
```
DisplayChangeListener displayChangeListener
```
Class OpenStackWindow extends StackWindow implements Serializable
- Serialized Fields
  - displayChangeListener
```
DisplayChangeListener displayChangeListener
```
Class Series_Labeler.FontPropertiesPanel extends Panel implements Serializable

Class Sync_Measure_3D extends Sync_Windows implements Serializable

Serialized Fields

DEFAULT_FIRST_SLICE
```
int DEFAULT_FIRST_SLICE
```
DEFAULT_LAST_SLICE
```
int DEFAULT_LAST_SLICE
```
measuring
```
boolean measuring
```
bMeasure
```
Button bMeasure
```
measurePanel
```
Panel measurePanel
```
mainPanelSize
```
int mainPanelSize
```
vScrollThresh
```
Vector<E> vScrollThresh
```
I_THRESH_SLIDER
```
String I_THRESH_SLIDER
```
vFirstButton
```
Vector<E> vFirstButton
```
I_FIRST_SLICE_BUTTON
```
String I_FIRST_SLICE_BUTTON
```
vFirstInt
```
Vector<E> vFirstInt
```
iFirstSlice
```
int[] iFirstSlice
```
I_FIRST_SLICE_BOX
```
String I_FIRST_SLICE_BOX
```
vLastButton
```
Vector<E> vLastButton
```
I_LAST_SLICE_BUTTON
```
String I_LAST_SLICE_BUTTON
```
vLastInt
```
Vector<E> vLastInt
```
iLastSlice
```
int[] iLastSlice
```
I_LAST_SLICE_BOX
```
String I_LAST_SLICE_BOX
```
bFirstSlice
```
Button bFirstSlice
```
intFirstSlice
```
IntField intFirstSlice
```
COMMON_FIRST_SLICE_BOX
```
String COMMON_FIRST_SLICE_BOX
```
bLastSlice
```
Button bLastSlice
```
intLastSlice
```
IntField intLastSlice
```
COMMON_LAST_SLICE_BOX
```
String COMMON_LAST_SLICE_BOX
```
bProjection
```
Button bProjection
```
hasProjection
```
boolean hasProjection
```
projection
```
ij.ImagePlus projection
```
resultsTable
```
Sync_Measure_3D.M3DRTab resultsTable
```
resultsWindow
```
Sync_Measure_3D.M3DRWin resultsWindow
```
nWindows
```
int nWindows
```
mOptions
```
int mOptions
```
nQuantities
```
int nQuantities
```
nRelQuantities
```
int nRelQuantities
```

Class Sync_Windows extends ij.plugin.frame.PlugInFrame implements Serializable
- Serialized Fields
 - vwins
```
Vector<E> vwins
```
 Indices of synchronized image windows are maintained in this Vector.
 - oldX
```
int oldX
```
 - oldY
```
int oldY
```
 - x
```
int x
```
 - y
```
int y
```
 - wList
```
List wList
```
 List of currently displayed windows retrieved from ImageJ window manager.
 - panel
```
Panel panel
```
 Panel for GUI
 - cCursor
```
Checkbox cCursor
```
 Checkboxes for user control.
 - cSlice
```
Checkbox cSlice
```
 Checkboxes for user control.
 - cChannel
```
Checkbox cChannel
```
 Checkboxes for user control.
 - cFrame
```
Checkbox cFrame
```
 Checkboxes for user control.
 - cCoords
```
Checkbox cCoords
```
 Checkboxes for user control.
 - cScaling
```
Checkbox cScaling
```
 Checkboxes for user control.
 - bSyncAll
```
Button bSyncAll
```
 Buttons for user control.
 - bUnsyncAll
```
Button bUnsyncAll
```
 Buttons for user control.
 - vListMap
```
Vector<E> vListMap
```
 Hashtable to map list ids to image window ids.
 - ijInstance
```
ij.ImageJ ijInstance
```
 reference to current instance of ImageJ (to avoid repeated IJ.getInstance() s)
 - currentMag
```
double currentMag
```
 - currentSrcRect
```
Rectangle currentSrcRect
```
 - bImage5DInstalled
```
boolean bImage5DInstalled
```
Class TextFieldFocus extends TextField implements Serializable
- Serialized Fields
  - currentText
```
String currentText
```
  - actionCommand
```
String actionCommand
```

Package ai
- Class ai.BalancedRandomForest extends AbstractClassifier implements Serializable
  - Serialized Fields
    - seed
```
int seed
```
      random seed
    - numTrees
```
int numTrees
```
      number of trees
    - numFeatures
```
int numFeatures
```
      number of features used on each node of the trees
    - tree
```
BalancedRandomTree[] tree
```
      array of random trees that form the forest
    - outOfBagError
```
double outOfBagError
```
      the out of bag error which has been calculated
- Class ai.BalancedRandomTree extends Object implements Serializable
  
  serialVersionUID:
  
  41518309467L
  - Serialized Fields
    - rootNode
```
ai.BalancedRandomTree.BaseNode rootNode
```
      root node
- Class ai.GiniFunction extends SplitFunction implements Serializable
  
  serialVersionUID:
  
  9707184791345L
  - Serialized Fields
    - index
```
int index
```
      index of the splitting attribute
    - threshold
```
double threshold
```
      threshold value of the splitting point
    - allSame
```
boolean allSame
```
      flag to identify when all samples belong to the same class
    - numOfFeatures
```
int numOfFeatures
```
      number of random features to use
    - random
```
Random random
```
      random number generator
- Class ai.InformationGainFunction extends SplitFunction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - numOfFeatures
```
int numOfFeatures
```
      number of random features to use
    - random
```
Random random
```
      random number generator
- Class ai.SplitFunction extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - index
```
int index
```
    - threshold
```
double threshold
```
    - allSame
```
boolean allSame
```
- Class ai.Splitter extends Object implements Serializable
  
  serialVersionUID:
  
  52652189902462L
  - Serialized Fields
    - template
```
SplitFunction template
```
      split function template
Package amira
- Class amira.AmiraTable extends ij.text.TextWindow implements Serializable
  - Serialized Fields
    - properties
```
Properties properties
```
    - show
```
boolean show
```
Package bdv.gui
- Class bdv.gui.BigWarpLandmarkPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 8470689265638231579L
 - Serialized Fields
 - tableModel
```
LandmarkTableModel tableModel
```
 - table
```
JTable table
```
 - logger
```
org.apache.log4j.Logger logger
```
- Class bdv.gui.BigWarpLandmarkPanel.JTableChecking extends JTable implements Serializable
 
 serialVersionUID:
 
 1437406384583869710L
- Class bdv.gui.BigWarpLandmarkPanel.TextFieldCell extends JTextField implements Serializable
 
 serialVersionUID:
 
 -4327183047476876882L
- Class bdv.gui.BigWarpLandmarkPanel.TextFieldCellEditor extends DefaultCellEditor implements Serializable
 
 serialVersionUID:
 
 9185738725311357320L
 - Serialized Fields
 - textField
```
BigWarpLandmarkPanel.TextFieldCell textField
```
 - columnClass
```
Class<T> columnClass
```
 - valueObject
```
Object valueObject
```
- Class bdv.gui.BigwarpLandmarkSelectionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 -6996547400011766393L
 - Serialized Fields
 - frame
```
JFrame frame
```
 - table
```
JTable table
```
 - selectionTable
```
BigwarpLandmarkSelectionPanel.PointSelectorTableModel selectionTable
```
 - doExport
```
boolean doExport
```
 - data
```
BigWarp.BigWarpData<T> data
```
 - sources
```
List<E> sources
```
 - fieldOfViewOption
```
String fieldOfViewOption
```
 - outputIntervalList
```
List<E> outputIntervalList
```
 - matchedPtNames
```
List<E> matchedPtNames
```
 - interp
```
Interpolation interp
```
 - offsetIn
```
double[] offsetIn
```
 - resolution
```
double[] resolution
```
 - isVirtual
```
boolean isVirtual
```
 - nThreads
```
int nThreads
```
 - progressWriter
```
ProgressWriter progressWriter
```
- Class bdv.gui.BigwarpLandmarkSelectionPanel.PointSelectorTableModel extends AbstractTableModel implements Serializable
 
 serialVersionUID:
 
 3826256129500169587L
 - Serialized Fields
 - selected
```
ArrayList<E> selected
```
 - names
```
ArrayList<E> names
```
- Class bdv.gui.BigWarpViewerFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 -7630931733043185034L
 - Serialized Fields
 - viewer
```
BigWarpViewerPanel viewer
```
 - keybindings
```
InputActionBindings keybindings
```
 - triggerbindings
```
TriggerBehaviourBindings triggerbindings
```
 - bw
```
BigWarp<T> bw
```
 - splitPanel
```
SplitPanel splitPanel
```
 - cards
```
CardPanel cards
```
 - setups
```
ConverterSetups setups
```
- Class bdv.gui.TransformTypeSelectDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - transformType
```
String transformType
```
 - tpsButton
```
JRadioButton tpsButton
```
 - affineButton
```
JRadioButton affineButton
```
 - similarityButton
```
JRadioButton similarityButton
```
 - rotationButton
```
JRadioButton rotationButton
```
 - translationButton
```
JRadioButton translationButton
```
Package bdv.ij
- Class bdv.ij.BigDataBrowserPlugIn.ThumbnailListRenderer extends DefaultListCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - font
```
Font font
```
Package bdv.img.openconnectome
- Class bdv.img.openconnectome.OpenConnectomeDataset extends Object implements Serializable
 
 serialVersionUID:
 
 7020249341572881545L
 - Serialized Fields
 - cube_dimension
```
HashMap<K,V> cube_dimension
```
 - description
```
String description
```
 - imagesize
```
HashMap<K,V> imagesize
```
 - neariso_imagesize
```
HashMap<K,V> neariso_imagesize
```
 - offset
```
HashMap<K,V> offset
```
 - neariso_offset
```
HashMap<K,V> neariso_offset
```
 - resolutions
```
int[] resolutions
```
 - voxelres
```
HashMap<K,V> voxelres
```
 - neariso_voxelres
```
HashMap<K,V> neariso_voxelres
```
- Class bdv.img.openconnectome.OpenConnectomeProject extends Object implements Serializable
 
 serialVersionUID:
 
 3296461682832630651L
 - Serialized Fields
 - dataset
```
String dataset
```
 - dataurl
```
String dataurl
```
 - dbname
```
String dbname
```
 - exceptions
```
boolean exceptions
```
 - host
```
String host
```
 - projecttype
```
int projecttype
```
 - readonly
```
boolean readonly
```
 - resolution
```
int resolution
```
- Class bdv.img.openconnectome.OpenConnectomeTokenInfo extends Object implements Serializable
 
 serialVersionUID:
 
 -560051267067033900L
 - Serialized Fields
 - dataset
```
OpenConnectomeDataset dataset
```
 - project
```
OpenConnectomeProject project
```
Package bdv.tools
- Class bdv.tools.HelpDialog extends DelayedPackDialog implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.tools.RecordMaxProjectionDialog extends DelayedPackDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - viewer
```
ViewerPanel viewer
```
 - maxTimepoint
```
int maxTimepoint
```
 - progressWriter
```
ProgressWriter progressWriter
```
 - pathTextField
```
JTextField pathTextField
```
 - spinnerMinTimepoint
```
JSpinner spinnerMinTimepoint
```
 - spinnerMaxTimepoint
```
JSpinner spinnerMaxTimepoint
```
 - spinnerWidth
```
JSpinner spinnerWidth
```
 - spinnerHeight
```
JSpinner spinnerHeight
```
 - spinnerStepSize
```
JSpinner spinnerStepSize
```
 - spinnerNumSteps
```
JSpinner spinnerNumSteps
```
- Class bdv.tools.RecordMovieDialog extends DelayedPackDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - viewer
```
ViewerPanel viewer
```
 - maxTimepoint
```
int maxTimepoint
```
 - progressWriter
```
ProgressWriter progressWriter
```
 - pathTextField
```
JTextField pathTextField
```
 - spinnerMinTimepoint
```
JSpinner spinnerMinTimepoint
```
 - spinnerMaxTimepoint
```
JSpinner spinnerMaxTimepoint
```
 - spinnerWidth
```
JSpinner spinnerWidth
```
 - spinnerHeight
```
JSpinner spinnerHeight
```
- Class bdv.tools.ToggleDialogAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - dialog
```
Dialog dialog
```
- Class bdv.tools.VisibilityAndGroupingDialog extends DelayedPackDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - visibilityPanel
```
VisibilityAndGroupingDialog.VisibilityPanel visibilityPanel
```
 Deprecated.
 - groupingPanel
```
VisibilityAndGroupingDialog.GroupingPanel groupingPanel
```
 Deprecated.
 - modePanel
```
VisibilityAndGroupingDialog.ModePanel modePanel
```
 Deprecated.
- Class bdv.tools.VisibilityAndGroupingDialog.GroupingPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - updateNames
```
ArrayList<E> updateNames
```
 - currentButtonsMap
```
Map<K,V> currentButtonsMap
```
 - updateActiveBoxes
```
ArrayList<E> updateActiveBoxes
```
 - updateAssignBoxes
```
ArrayList<E> updateAssignBoxes
```
 - state
```
ViewerState state
```
 - isVisible
```
BooleanSupplier isVisible
```
 - recreateContentPending
```
AtomicBoolean recreateContentPending
```
 - updateGroupNamesPending
```
AtomicBoolean updateGroupNamesPending
```
 - updateGroupAssignmentsPending
```
AtomicBoolean updateGroupAssignmentsPending
```
 - updateGroupActivityPending
```
AtomicBoolean updateGroupActivityPending
```
 - updateCurrentGroupPending
```
AtomicBoolean updateCurrentGroupPending
```
- Class bdv.tools.VisibilityAndGroupingDialog.ModePanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - state
```
ViewerState state
```
 - groupingBox
```
JCheckBox groupingBox
```
 - fusedModeBox
```
JCheckBox fusedModeBox
```
 - isVisible
```
BooleanSupplier isVisible
```
 - updatePending
```
AtomicBoolean updatePending
```
- Class bdv.tools.VisibilityAndGroupingDialog.VisibilityPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - state
```
ViewerState state
```
 - currentButtonsMap
```
Map<K,V> currentButtonsMap
```
 - updateActiveBoxes
```
ArrayList<E> updateActiveBoxes
```
 - updateVisibleBoxes
```
ArrayList<E> updateVisibleBoxes
```
 - isVisible
```
BooleanSupplier isVisible
```
 - recreateContentPending
```
AtomicBoolean recreateContentPending
```
 - updatePending
```
AtomicBoolean updatePending
```
Package bdv.tools.boundingbox
- Class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - buttons
```
AbstractTransformedBoxSelectionDialog.OkCancelPanel buttons
```
 - result
```
Object result
```
 - monitor
```
Object monitor
```
- Class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.OkCancelPanel extends JPanel implements Serializable
 - Serialized Fields
 - runOnOk
```
ArrayList<E> runOnOk
```
 - runOnCancel
```
ArrayList<E> runOnCancel
```
- Class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel extends JPanel implements Serializable
 - Serialized Fields
 - timeRange
```
BoundedInterval timeRange
```
 - timeValue
```
BoundedValue timeValue
```
 - mode
```
BoxSelectionOptions.TimepointSelection mode
```
- Class bdv.tools.boundingbox.BoundingBoxDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - interval
```
ModifiableInterval interval
```
 Deprecated.
 - boxRealRandomAccessible
```
BoxRealRandomAccessible<T extends Type<T>> boxRealRandomAccessible
```
 Deprecated.
 - boxSelectionPanel
```
BoxSelectionPanel boxSelectionPanel
```
 Deprecated.
 - boxSourceAndConverter
```
SourceAndConverter<T> boxSourceAndConverter
```
 Deprecated.
 - boxConverterSetup
```
RealARGBColorConverterSetup boxConverterSetup
```
 Deprecated.
 - boxOverlay
```
TransformedBoxOverlay boxOverlay
```
 Deprecated.
 - contentCreated
```
boolean contentCreated
```
 Deprecated.
- Class bdv.tools.boundingbox.BoxDisplayModePanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.tools.boundingbox.BoxSelectionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - ranges
```
BoundedInterval[] ranges
```
 - minSliderPanels
```
SliderPanel[] minSliderPanels
```
 - maxSliderPanels
```
SliderPanel[] maxSliderPanels
```
 - selection
```
BoxSelectionPanel.Box selection
```
 - cols
```
int cols
```
 - n
```
int n
```
- Class bdv.tools.boundingbox.RealBoxSelectionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - ranges
```
BoundedIntervalDouble[] ranges
```
 - minSliderPanels
```
SliderPanelDouble[] minSliderPanels
```
 - maxSliderPanels
```
SliderPanelDouble[] maxSliderPanels
```
 - selection
```
RealBoxSelectionPanel.RealBox selection
```
 - cols
```
int cols
```
 - n
```
int n
```
- Class bdv.tools.boundingbox.TransformedBoxSelectionDialog extends AbstractTransformedBoxSelectionDialog<TransformedBoxSelectionDialog.Result> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
TransformedBoxModel model
```
 - boxEditor
```
TransformedBoxEditor boxEditor
```
 - content
```
JPanel content
```
 - viewer
```
ViewerPanel viewer
```
 - boxSelectionPanel
```
BoxSelectionPanel boxSelectionPanel
```
 - timepointSelectionPanel
```
AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel timepointSelectionPanel
```
 - options
```
BoxSelectionOptions options
```
- Class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog extends AbstractTransformedBoxSelectionDialog<TransformedRealBoxSelectionDialog.Result> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
TransformedRealBoxModel model
```
 - boxEditor
```
TransformedBoxEditor boxEditor
```
 - content
```
JPanel content
```
 - viewer
```
ViewerPanel viewer
```
 - boxSelectionPanel
```
RealBoxSelectionPanel boxSelectionPanel
```
 - timepointSelectionPanel
```
AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel timepointSelectionPanel
```
 - options
```
BoxSelectionOptions options
```
Package bdv.tools.brightness
- Class bdv.tools.brightness.BrightnessDialog extends DelayedPackDialog implements Serializable
 
 serialVersionUID:
 
 7963632306732311403L
- Class bdv.tools.brightness.BrightnessDialog.ColorsPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 6408468837346789676L
 - Serialized Fields
 - setupAssignments
```
SetupAssignments setupAssignments
```
 - buttons
```
ArrayList<E> buttons
```
 - colorChooser
```
JColorChooser colorChooser
```
- Class bdv.tools.brightness.BrightnessDialog.MinMaxPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 -5209143847804383789L
 - Serialized Fields
 - setupAssignments
```
SetupAssignments setupAssignments
```
 - minMaxGroup
```
MinMaxGroup minMaxGroup
```
 - boxes
```
ArrayList<E> boxes
```
 - sliders
```
JPanel sliders
```
 - showAdvanced
```
Runnable showAdvanced
```
 - hideAdvanced
```
Runnable hideAdvanced
```
 - isShowingAdvanced
```
boolean isShowingAdvanced
```
 - rememberSizes
```
boolean rememberSizes
```
- Class bdv.tools.brightness.BrightnessDialog.MinMaxPanels extends JPanel implements Serializable
 
 serialVersionUID:
 
 6538962298579455010L
 - Serialized Fields
 - setupAssignments
```
SetupAssignments setupAssignments
```
 - minMaxPanels
```
ArrayList<E> minMaxPanels
```
 - dialog
```
JDialog dialog
```
 - rememberSizes
```
boolean rememberSizes
```
 - isShowingAdvanced
```
boolean isShowingAdvanced
```
- Class bdv.tools.brightness.SliderPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 6444334522127424416L
 - Serialized Fields
 - slider
```
JSlider slider
```
 - spinner
```
JSpinner spinner
```
 - model
```
BoundedValue model
```
- Class bdv.tools.brightness.SliderPanelDouble extends JPanel implements Serializable
 
 serialVersionUID:
 
 6444334522127424416L
 - Serialized Fields
 - slider
```
JSlider slider
```
 - spinner
```
JSpinner spinner
```
 - model
```
BoundedValueDouble model
```
 - dmin
```
double dmin
```
 - dmax
```
double dmax
```
 - userDefinedNumberFormat
```
boolean userDefinedNumberFormat
```
 - rangeListener
```
SliderPanelDouble.RangeListener rangeListener
```

Package bdv.tools.crop

Class bdv.tools.crop.CropDialog extends JDialog implements Serializable

serialVersionUID:: 924395364255873920L

Serialized Fields

viewer
```
ViewerPanel viewer
```

sequenceDescription

AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader> sequenceDescription

pathTextField
```
JTextField pathTextField
```
spinnerMinTimepoint
```
JSpinner spinnerMinTimepoint
```
spinnerMaxTimepoint
```
JSpinner spinnerMaxTimepoint
```

Package bdv.ui.convertersetupeditor
- Class bdv.ui.convertersetupeditor.ConverterSetupEditPanel extends JPanel implements Serializable
  - Serialized Fields
    - colorPanel
```
bdv.ui.convertersetupeditor.ColorPanel colorPanel
```
    - rangePanel
```
bdv.ui.convertersetupeditor.BoundedRangePanel rangePanel
```
Package bdv.ui.rangeslider
- Class bdv.ui.rangeslider.RangeSlider extends JSlider implements Serializable
  
  serialVersionUID:
  
  1L
Package bdv.ui.sourcegrouptree
- Class bdv.ui.sourcegrouptree.SourceGroupTree extends JTree implements Serializable
  - Serialized Fields
    - state
```
ViewerState state
```
    - model
```
SourceGroupTreeModel model
```
    - renderer
```
bdv.ui.sourcegrouptree.SourceGroupTreeCellRenderer renderer
```
    - editor
```
bdv.ui.sourcegrouptree.SourceGroupEditor editor
```
    - focusedSelectionBg
```
Color focusedSelectionBg
```
    - unfocusedSelectionBg
```
Color unfocusedSelectionBg
```
    - pressedAt
```
Point pressedAt
```
    - consumeNext
```
boolean consumeNext
```
    - releasedWhen
```
long releasedWhen
```
- Class bdv.ui.sourcegrouptree.SourceGroupTree.SourceGroupTreeTransferHandler extends TransferHandler implements Serializable
  - Serialized Fields
    - tree
```
SourceGroupTree tree
```
    - state
```
ViewerState state
```
Package bdv.ui.sourcetable
- Class bdv.ui.sourcetable.SourceTable extends JTable implements Serializable
  - Serialized Fields
    - model
```
SourceTableModel model
```
    - state
```
ViewerState state
```
    - converters
```
SourceToConverterSetupBimap converters
```
    - focusedSelectionBg
```
Color focusedSelectionBg
```
    - unfocusedSelectionBg
```
Color unfocusedSelectionBg
```
    - focusedSelectionFg
```
Color focusedSelectionFg
```
    - pressedAt
```
Point pressedAt
```
    - consumeNext
```
boolean consumeNext
```
    - releasedWhen
```
long releasedWhen
```
- Class bdv.ui.sourcetable.SourceTableModel extends AbstractTableModel implements Serializable
  - Serialized Fields
    - state
```
ViewerState state
```
    - converters
```
SourceToConverterSetupBimap converters
```
    - model
```
bdv.ui.sourcetable.SourceTableModel.StateModel model
```
Package bdv.ui.splitpanel
- Class bdv.ui.splitpanel.SplitPanel extends JSplitPane implements Serializable
  - Serialized Fields
    - scrollPane
```
JScrollPane scrollPane
```
    - width
```
int width
```
    - oneTouchExpandAnimator
```
bdv.ui.splitpanel.SplitPaneOneTouchExpandAnimator oneTouchExpandAnimator
```
    - dividerSizeWhenVisible
```
int dividerSizeWhenVisible
```

Package bdv.ui.viewermodepanel

Class bdv.ui.viewermodepanel.DisplaySettingsPanel extends JPanel implements Serializable

Serialized Fields

fusion

bdv.ui.viewermodepanel.LabeledToggleButton fusion

grouping

bdv.ui.viewermodepanel.LabeledToggleButton grouping

interpolation

bdv.ui.viewermodepanel.LabeledToggleButton interpolation

Package bdv.util
- Class bdv.util.DelayedPackDialog extends JDialog implements Serializable
  - Serialized Fields
    - packIsPending
```
boolean packIsPending
```
Package bdv.viewer
- Class bdv.viewer.BigWarpLandmarkFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 -5160678226566479257L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - lmPanel
```
BigWarpLandmarkPanel lmPanel
```
 - keybindings
```
InputActionBindings keybindings
```
- Class bdv.viewer.BigWarpViewerPanel extends ViewerPanel implements Serializable
 
 serialVersionUID:
 
 7706602964307210070L
 - Serialized Fields
 - sources
```
List<E> sources
```
 - viewerSettings
```
BigWarpViewerSettings viewerSettings
```
 - overlay
```
BigWarpOverlay overlay
```
 - dragOverlay
```
BigWarpDragOverlay dragOverlay
```
 - message
```
MessageOverlayAnimator message
```
 - isMoving
```
boolean isMoving
```
 - updateOnDrag
```
boolean updateOnDrag
```
 - transformEnabled
```
boolean transformEnabled
```
 - ndims
```
int ndims
```
 - movingSourceIndexList
```
int[] movingSourceIndexList
```
 - targetSourceIndexList
```
int[] targetSourceIndexList
```
 - boxOverlayVisible
```
boolean boxOverlayVisible
```
 - textOverlayVisible
```
boolean textOverlayVisible
```
 - orthoTransforms
```
ArrayList<E> orthoTransforms
```
 - options
```
ViewerOptions options
```
- Class bdv.viewer.InteractiveDisplayCanvas extends JComponent implements Serializable
 - Serialized Fields
 - handler
```
TransformEventHandler handler
```
 Mouse/Keyboard handler that manipulates the view transformation.
 - overlayRenderers
```
org.scijava.listeners.Listeners.List<T> overlayRenderers
```
 To draw this component, OverlayRenderer.drawOverlays(java.awt.Graphics) is invoked for each renderer.
- Class bdv.viewer.LandmarkPointMenu extends JPopupMenu implements Serializable
 
 serialVersionUID:
 
 -3676180390835767585L
 - Serialized Fields
 - landmarkPanel
```
BigWarpLandmarkPanel landmarkPanel
```
 - bw
```
BigWarp<T> bw
```
 - clearSelectedMoving
```
LandmarkPointMenu.ClearSelectedHandler clearSelectedMoving
```
 - clearSelectedFixed
```
LandmarkPointMenu.ClearSelectedHandler clearSelectedFixed
```
 - deleteSelectedHandler
```
LandmarkPointMenu.DeleteSelectedHandler deleteSelectedHandler
```
 - activateAllHandler
```
LandmarkPointMenu.ActivateSelectedHandler activateAllHandler
```
 - deactivateAllHandler
```
LandmarkPointMenu.DeactivateSelectedHandler deactivateAllHandler
```
 - popupListener
```
MouseListener popupListener
```
 - deleteAllItem
```
JMenuItem deleteAllItem
```
 - activateAllItem
```
JMenuItem activateAllItem
```
 - deactivateAllItem
```
JMenuItem deactivateAllItem
```
 - clearSelectedMovingItem
```
JMenuItem clearSelectedMovingItem
```
 - clearSelectedFixedItem
```
JMenuItem clearSelectedFixedItem
```
 - clickPt
```
Point clickPt
```
- Class bdv.viewer.LandmarkPointMenu.ActivateSelectedHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 3617611493865908091L
- Class bdv.viewer.LandmarkPointMenu.ClearHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -2082631635521009679L
 - Serialized Fields
 - moving
```
boolean moving
```
- Class bdv.viewer.LandmarkPointMenu.ClearSelectedHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -7023942870606943587L
 - Serialized Fields
 - moving
```
boolean moving
```
- Class bdv.viewer.LandmarkPointMenu.DeactivateSelectedHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -7703797647219426189L
- Class bdv.viewer.LandmarkPointMenu.DeleteHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -3405442710985689438L
- Class bdv.viewer.LandmarkPointMenu.DeleteSelectedHandler extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -6499718644014842587L
- Class bdv.viewer.ViewerFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - viewer
```
ViewerPanel viewer
```
 - cards
```
CardPanel cards
```
 - splitPanel
```
SplitPanel splitPanel
```
 - keybindings
```
InputActionBindings keybindings
```
 - triggerbindings
```
TriggerBehaviourBindings triggerbindings
```
 - setups
```
ConverterSetups setups
```
- Class bdv.viewer.ViewerPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - state
```
ViewerState state
```
 Currently rendered state (visible sources, transformation, timepoint, etc.) A copy can be obtained by ViewerPanel.getState().
 - imageRenderer
```
MultiResolutionRenderer imageRenderer
```
 Renders the current state for the ViewerPanel.display.
 - renderTarget
```
BufferedImageOverlayRenderer renderTarget
```
 TODO
 - multiBoxOverlayRenderer
```
MultiBoxOverlayRenderer multiBoxOverlayRenderer
```
 Overlay navigation boxes.
 - sourceInfoOverlayRenderer
```
SourceInfoOverlayRenderer sourceInfoOverlayRenderer
```
 Overlay current source name and current timepoint.
 - scaleBarOverlayRenderer
```
ScaleBarOverlayRenderer scaleBarOverlayRenderer
```
 TODO
 - transformEventHandler
```
TransformEventHandler transformEventHandler
```
 - display
```
InteractiveDisplayCanvas display
```
 Canvas used for displaying the rendered image and overlays.
 - sliderTime
```
JSlider sliderTime
```
 - blockSliderTimeEvents
```
boolean blockSliderTimeEvents
```
 - threadGroup
```
ThreadGroup threadGroup
```
 A ThreadGroup for (only) the threads used by this ViewerPanel, that is, ViewerPanel.painterThread and ViewerPanel.renderingExecutorService.
 - painterThread
```
PainterThread painterThread
```
 Thread that triggers repainting of the display.
 - renderingExecutorService
```
ExecutorService renderingExecutorService
```
 The ExecutorService used for rendereing.
 - mouseCoordinates
```
ViewerPanel.MouseCoordinateListener mouseCoordinates
```
 Keeps track of the current mouse coordinates, which are used to provide the current global position (see ViewerPanel.getGlobalMouseCoordinates(RealPositionable)).
 - visibilityAndGrouping
```
VisibilityAndGrouping visibilityAndGrouping
```
 Manages visibility and currentness of sources and groups, as well as grouping of sources, and display mode.
 - transformListeners
```
CopyOnWriteArrayList<E> transformListeners
```
 These listeners will be notified about changes to the viewer-transform. This is done before calling ViewerPanel.requestRepaint() so listeners have the chance to interfere.
 - timePointListeners
```
CopyOnWriteArrayList<E> timePointListeners
```
 These listeners will be notified about changes to the current timepoint ViewerState.getCurrentTimepoint(). This is done before calling ViewerPanel.requestRepaint() so listeners have the chance to interfere.
 - interpolationModeListeners
```
CopyOnWriteArrayList<E> interpolationModeListeners
```
 - currentAnimator
```
AbstractTransformAnimator currentAnimator
```
 Current animator for viewer transform, or null. This is for example used to make smooth transitions when aligning to orthogonal planes.
 - overlayAnimators
```
ArrayList<E> overlayAnimators
```
 A list of currently incomplete (see OverlayAnimator.isComplete()) animators. Initially, this contains a TextOverlayAnimator showing the "press F1 for help" message.
 - msgOverlay
```
MessageOverlayAnimator msgOverlay
```
 Fade-out overlay of recent messages. See ViewerPanel.showMessage(String).
 - options
```
ViewerOptions.Values options
```
- Class bdv.viewer.WarpNavigationActions.AlignPlaneAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 -5868085804210873492L
 - Serialized Fields
 - plane
```
ViewerPanel.AlignPlane plane
```
- Class bdv.viewer.WarpNavigationActions.CardAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 -8949725696799894130L
 - Serialized Fields
 - frame
```
BigWarpViewerFrame frame
```
- Class bdv.viewer.WarpNavigationActions.CollapseCardAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 -2337698189753056286L
 - Serialized Fields
 - frame
```
BigWarpViewerFrame frame
```
- Class bdv.viewer.WarpNavigationActions.DisplayXfmAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.viewer.WarpNavigationActions.ExpandCardAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 -4267852269622298980L
 - Serialized Fields
 - frame
```
BigWarpViewerFrame frame
```
- Class bdv.viewer.WarpNavigationActions.RotatePlaneAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - direction
```
WarpNavigationActions.rotationDirections2d direction
```
- Class bdv.viewer.WarpNavigationActions.SetCurrentSourceOrGroupAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - index
```
int index
```
- Class bdv.viewer.WarpNavigationActions.ToggleFusedModeAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.viewer.WarpNavigationActions.ToggleGroupingAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.viewer.WarpNavigationActions.ToggleInterPolationAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
- Class bdv.viewer.WarpNavigationActions.ToggleSourceOrGroupVisibilityAction extends bdv.viewer.WarpNavigationActions.NavigationAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - index
```
int index
```
Package bdv.viewer.animate
- Class bdv.viewer.animate.SimilarityModel3D extends AbstractAffineModel3D<SimilarityModel3D> implements Serializable
 
 serialVersionUID:
 
 5509363764217496393L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m03
```
double m03
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m13
```
double m13
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - m23
```
double m23
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - i02
```
double i02
```
 - i03
```
double i03
```
 - i10
```
double i10
```
 - i11
```
double i11
```
 - i12
```
double i12
```
 - i13
```
double i13
```
 - i20
```
double i20
```
 - i21
```
double i21
```
 - i22
```
double i22
```
 - i23
```
double i23
```
 - N
```
double[][] N
```
 - isInvertible
```
boolean isInvertible
```
Package bigwarp
- Class bigwarp.BigWarp.WarningTableCellRenderer extends DefaultTableCellRenderer implements Serializable
 
 serialVersionUID:
 
 7836269349663370123L
- Class bigwarp.BigWarpActions.AlignViewerPanelAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -7023242695323421450L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - type
```
BigWarpActions.AlignViewerPanelAction.TYPE type
```
- Class bigwarp.BigWarpActions.DebugAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 7408679512565343805L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.EstimateWarpAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -210012348709096037L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ExportAffineAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 9190515918045510236L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ExportImagePlusAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -8109832912959931917L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ExportWarpAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 4626378501415886468L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.GarbageCollectionAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -4487441057212703143L
- Class bigwarp.BigWarpActions.GoToBookmarkAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 8777199828772379323L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.GoToBookmarkRotationAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -6169895035295179820L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.LandmarkGridDialogAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.LandmarkModeAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 4079013525930019558L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - isOn
```
boolean isOn
```
- Class bigwarp.BigWarpActions.LoadLandmarksAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -5405137757290988030L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.LoadSettingsAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.PrintTransformAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 6065343788485350279L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.QuickSaveLandmarksAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -4761309639234262643L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ResetActiveViewerAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -130575800163574517L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.SaveLandmarksAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 7897687176745034315L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.SaveSettingsAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.SaveWarpedAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 4965249994677649713L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 Deprecated.
- Class bigwarp.BigWarpActions.SaveWarpedXmlAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -5437508072904256758L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.SetBookmarkAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -4060308986781809606L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.SetWarpMagBaseAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 7370813069619338918L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - i
```
int i
```
- Class bigwarp.BigWarpActions.SetWarpVisGridTypeAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 7370813069619338918L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - type
```
GridSource.GRID_TYPE type
```
- Class bigwarp.BigWarpActions.SetWarpVisTypeAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 7370813069619338918L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - p
```
BigWarpViewerFrame p
```
 - type
```
BigWarp.WarpVisType type
```
- Class bigwarp.BigWarpActions.TableSelectionAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -4647679094757721276L
 - Serialized Fields
 - table
```
JTable table
```
 - selection
```
int selection
```
- Class bigwarp.BigWarpActions.ToggleAlwaysEstimateTransformAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 2909830484701853577L
 - Serialized Fields
 - bwvp
```
BigWarpViewerFrame bwvp
```
- Class bigwarp.BigWarpActions.ToggleBoxAndTexOverlayVisibility extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -900781969157241037L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ToggleLandmarkModeAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 234323425930019L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.ToggleMovingImageDisplayAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 6495981071796613953L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.TogglePointNameVisibleAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 2639535533224809586L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.TogglePointsVisibleAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 8747830204501341125L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.UndoRedoAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 -5413579107763110117L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - isRedo
```
boolean isRedo
```
- Class bigwarp.BigWarpActions.WarpToNearest extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 3244181492305479433L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.BigWarpActions.WarpToNextAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 8515568118251877405L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - inc
```
int inc
```
- Class bigwarp.BigWarpActions.WarpToSelectedAction extends AbstractNamedAction implements Serializable
 
 serialVersionUID:
 
 5233843444920094805L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
- Class bigwarp.HelpDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 1L
- Class bigwarp.SourceInfoDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 8333668892181971701L
- Class bigwarp.WarpVisFrame extends JDialog implements Serializable
 
 serialVersionUID:
 
 7561228647761694686L
 - Serialized Fields
 - bw
```
BigWarp<T> bw
```
 - settings
```
BigWarpViewerSettings settings
```
 - visTypeGroup
```
ButtonGroup visTypeGroup
```
 - setWarpVisOffButton
```
JRadioButton setWarpVisOffButton
```
 - setWarpGridButton
```
JRadioButton setWarpGridButton
```
 - setWarpMagButton
```
JRadioButton setWarpMagButton
```
 - noOptionsLabel
```
JLabel noOptionsLabel
```
 - landmarkColorButton
```
JButton landmarkColorButton
```
 - colorChooser
```
JColorChooser colorChooser
```
 - landmarkSizeSlider
```
JSlider landmarkSizeSlider
```
 - warpMagButtons
```
ButtonGroup warpMagButtons
```
 - warpMagAffineButton
```
JRadioButton warpMagAffineButton
```
 - warpMagSimilarityButton
```
JRadioButton warpMagSimilarityButton
```
 - warpMagRigidButton
```
JRadioButton warpMagRigidButton
```
 - warpGridButtons
```
ButtonGroup warpGridButtons
```
 - warpGridLineButton
```
JRadioButton warpGridLineButton
```
 - warpGridModButton
```
JRadioButton warpGridModButton
```
 - gridSpacingSlider
```
JSlider gridSpacingSlider
```
 - gridWidthSlider
```
JSlider gridWidthSlider
```
 - bigSpace
```
Component bigSpace
```
 - smallSpace
```
Component smallSpace
```
 - gridSpacingLabel
```
JLabel gridSpacingLabel
```
 - gridWidthLabel
```
JLabel gridWidthLabel
```
 - savePeriodModel
```
SpinnerNumberModel savePeriodModel
```
 - autoSavePeriodSpinner
```
JSpinner autoSavePeriodSpinner
```
 - doAutoSaveBox
```
JCheckBox doAutoSaveBox
```
 - autoSaveFolderText
```
JTextField autoSaveFolderText
```

Package bigwarp.landmarks

Class bigwarp.landmarks.LandmarkTableModel extends AbstractTableModel implements Serializable

serialVersionUID:: -5865789085410559166L

Serialized Fields

PENDING_PT
```
double[] PENDING_PT
```
DEBUG
```
boolean DEBUG
```
ndims
```
int ndims
```
numCols
```
int numCols
```
numRows
```
int numRows
```
nextRowP
```
int nextRowP
```
nextRowQ
```
int nextRowQ
```
numActive
```
int numActive
```
names
```
ArrayList<E> names
```
activeList
```
ArrayList<E> activeList
```
movingPts
```
ArrayList<E> movingPts
```
targetPts
```
ArrayList<E> targetPts
```
tableIndexToActiveIndex
```
ArrayList<E> tableIndexToActiveIndex
```
pointUpdatePending
```
boolean pointUpdatePending
```
pointUpdatePendingMoving
```
boolean pointUpdatePendingMoving
```
pointToOverride
```
Double[] pointToOverride
```
doesPointHaveAndNeedWarp
```
ArrayList<E> doesPointHaveAndNeedWarp
```
indicesOfChangedPoints
```
ArrayList<E> indicesOfChangedPoints
```
elementDeleted
```
boolean elementDeleted
```
needsInverse
```
ArrayList<E> needsInverse
```

movingDisplayPointUnreliable

ArrayList<E> movingDisplayPointUnreliable

estimatedXfm

ThinPlateR2LogRSplineKernelTransform estimatedXfm

warpedPoints
```
ArrayList<E> warpedPoints
```
maxInverseIterations
```
int maxInverseIterations
```
inverseThreshold
```
double inverseThreshold
```
lastPoint
```
double[] lastPoint
```
tmp
```
double[] tmp
```
undoRedoManager
```
LandmarkUndoManager undoRedoManager
```
message
```
BigWarpMessageAnimator message
```
modifiedSinceLastSave
```
boolean modifiedSinceLastSave
```
columnNames
```
String[] columnNames
```
logger
```
org.apache.log4j.Logger logger
```

Package bigwarp.landmarks.actions
- Class bigwarp.landmarks.actions.AbstractPointEdit extends AbstractUndoableEdit implements Serializable
  
  serialVersionUID:
  
  6129026885209095156L
  - Serialized Fields
    - ltm
```
LandmarkTableModel ltm
```
- Class bigwarp.landmarks.actions.AddPointEdit extends AbstractPointEdit implements Serializable
  
  serialVersionUID:
  
  3080160649652516963L
  - Serialized Fields
    - index
```
int index
```
    - newpt
```
double[] newpt
```
    - isMoving
```
boolean isMoving
```
- Class bigwarp.landmarks.actions.DeleteRowEdit extends AbstractPointEdit implements Serializable
  
  serialVersionUID:
  
  -3624020789748090982L
  - Serialized Fields
    - index
```
int index
```
    - movingPt
```
double[] movingPt
```
    - targetPt
```
double[] targetPt
```
- Class bigwarp.landmarks.actions.LandmarkUndoManager extends UndoManager implements Serializable
  
  serialVersionUID:
  
  -2126698066459744227L
- Class bigwarp.landmarks.actions.ModifyPointEdit extends AbstractPointEdit implements Serializable
  
  serialVersionUID:
  
  6962786164691889547L
  - Serialized Fields
    - index
```
int index
```
    - oldpt
```
double[] oldpt
```
    - newpt
```
double[] newpt
```
    - isMoving
```
boolean isMoving
```
Package Bug_Submitter
- Class Bug_Submitter.NewBugDialog.RedoAction extends AbstractAction implements Serializable
- Class Bug_Submitter.NewBugDialog.UndoAction extends AbstractAction implements Serializable
Package bunwarpj
- Class bunwarpj.ClearAll extends Dialog implements Serializable
 
 serialVersionUID:
 
 2082815245983765787L
 - Serialized Fields
 - sourcePh
```
PointHandler sourcePh
```
 point handler for source image
 - targetPh
```
PointHandler targetPh
```
 point handler for target image
- Class bunwarpj.CumulativeQueue extends Vector<Double> implements Serializable
 
 serialVersionUID:
 
 -1862591645420274411L
 - Serialized Fields
 - ridx
```
int ridx
```
 front index of the queue
 - widx
```
int widx
```
 rear index of the queue
 - currentLength
```
int currentLength
```
 current length of the queue
 - sum
```
double sum
```
 queue sum
- Class bunwarpj.IODialog extends Dialog implements Serializable
 
 serialVersionUID:
 
 2016840469406208859L
 - Serialized Fields
 - sourceImp
```
ij.ImagePlus sourceImp
```
 Pointer to the source image representation
 - targetImp
```
ij.ImagePlus targetImp
```
 Pointer to the target image representation
 - sourcePh
```
PointHandler sourcePh
```
 Point handler for the source image
 - targetPh
```
PointHandler targetPh
```
 Point handler for the target image
 - dialog
```
MainDialog dialog
```
 Dialog for bUnwarpJ interface
- Class bunwarpj.MainDialog extends GenericDialog implements Serializable
 
 serialVersionUID:
 
 8828022405402308341L
 - Serialized Fields
 - imageList
```
ij.ImagePlus[] imageList
```
 List of available images in ImageJ
 - sourceIc
```
ImageCanvas sourceIc
```
 Canvas of the source image
 - targetIc
```
ImageCanvas targetIc
```
 Canvas of the target image
 - sourceImp
```
ij.ImagePlus sourceImp
```
 Image representation for source image
 - targetImp
```
ij.ImagePlus targetImp
```
 Image representation for target image
 - originalSourceIP
```
ij.process.ImageProcessor originalSourceIP
```
 initial source image processor
 - originalTargetIP
```
ij.process.ImageProcessor originalTargetIP
```
 initial target image processor
 - source
```
BSplineModel source
```
 Model for source image
 - target
```
BSplineModel target
```
 Model for target image
 - sourceMsk
```
Mask sourceMsk
```
 Mask for source image
 - targetMsk
```
Mask targetMsk
```
 Mask for target image
 - sourceAffineMatrix
```
double[][] sourceAffineMatrix
```
 Initial affine matrix for the source image
 - targetAffineMatrix
```
double[][] targetAffineMatrix
```
 Initial affine matrix for the target image
 - sourcePh
```
PointHandler sourcePh
```
 Point handlers for the landmarks in the source image
 - targetPh
```
PointHandler targetPh
```
 Point handlers for the landmarks in the target image
 - clearMask
```
boolean clearMask
```
 Boolean for clearing mask
 - tb
```
PointToolbar tb
```
 Toolbar handler
 - finalActionLaunched
```
boolean finalActionLaunched
```
 flag to see if the finalAction was launched
 - stopRegistration
```
boolean stopRegistration
```
 flag to stop the registration
 - sourceChoiceIndex
```
int sourceChoiceIndex
```
 index of the source choice
 - targetChoiceIndex
```
int targetChoiceIndex
```
 index of the target choice
 - min_scale_deformation
```
int min_scale_deformation
```
 minimum scale deformation
 - max_scale_deformation
```
int max_scale_deformation
```
 maximum scale deformation
 - mode
```
int mode
```
 mode ("Accurate" by default)
 - maxImageSubsamplingFactor
```
int maxImageSubsamplingFactor
```
 image subsampling factor at highest resolution level
 - divWeight
```
double divWeight
```
 divergence weight
 - curlWeight
```
double curlWeight
```
 curl weight
 - landmarkWeight
```
double landmarkWeight
```
 landmarks weight
 - imageWeight
```
double imageWeight
```
 image similarity weight
 - consistencyWeight
```
double consistencyWeight
```
 consistency weight
 - richOutput
```
boolean richOutput
```
 flag for rich output (verbose option)
 - saveTransformation
```
boolean saveTransformation
```
 flag for save transformation option
 - min_scale_image
```
int min_scale_image
```
 minimum image scale
 - imagePyramidDepth
```
int imagePyramidDepth
```
 maximum depth for the image pyramid
 - stopThreshold
```
double stopThreshold
```
 stopping threshold
 - bIsReverse
```
boolean bIsReverse
```
 consistency flag (if false, unidirectional registration is done)
 - bMacro
```
boolean bMacro
```
 macro flag
 - macroArgs
```
String macroArgs
```
 macro arguments
 - previousSourceRoi
```
Roi previousSourceRoi
```
 region of interest of the source image before calling the plugin
 - previousTargetRoi
```
Roi previousTargetRoi
```
 region of interest of the target image before calling the plugin
 - sourceChoice
```
Choice sourceChoice
```
 source image choice
 - targetChoice
```
Choice targetChoice
```
 target image choice
 - minScaleChoice
```
Choice minScaleChoice
```
 minimum scale choice
 - maxScaleChoice
```
Choice maxScaleChoice
```
 maximum scale choice
 - modeChoice
```
Choice modeChoice
```
 accurate mode choice
 - resamplingTextField
```
TextField resamplingTextField
```
 resampling text field
 - resamplingSlider
```
Scrollbar resamplingSlider
```
 resampling scroll bar
 - consistencyWeightTextField
```
TextField consistencyWeightTextField
```
 consistency weight text field
- Class bunwarpj.PointAction extends ImageCanvas implements Serializable
 
 serialVersionUID:
 
 -8141177836023328859L
 - Serialized Fields
 - mainImp
```
ij.ImagePlus mainImp
```
 main image plus (active image)
 - secondaryImp
```
ij.ImagePlus secondaryImp
```
 secondary image plus (the other image involved in the registration)
 - mainPh
```
PointHandler mainPh
```
 main point handler (set of points of the active image)
 - secondaryPh
```
PointHandler secondaryPh
```
 secondary point handler (set of point of the other image)
 - tb
```
PointToolbar tb
```
 pointer to the toolbar
 - dialog
```
MainDialog dialog
```
 pointer to the interface dialog
 - mouseDownTime
```
long mouseDownTime
```
 time the mouse is down
- Class bunwarpj.PointHandler extends Roi implements Serializable
 
 serialVersionUID:
 
 4829296689557078996L
 - Serialized Fields
 - listColors
```
Vector<E> listColors
```
 - listPoints
```
Vector<E> listPoints
```
 list of points
 - currentPoint
```
int currentPoint
```
 current point
 - numPoints
```
int numPoints
```
 number of points
 - started
```
boolean started
```
 start flag
 - listMaskPoints
```
Vector<E> listMaskPoints
```
 list of points in the mask
 - maskClosed
```
boolean maskClosed
```
 flat to check if the mask is closed or not
 - imp
```
ij.ImagePlus imp
```
 pointer to the image representation
 - pa
```
PointAction pa
```
 pointer to the point actions
 - tb
```
PointToolbar tb
```
 pointer to the point toolbar
 - mask
```
Mask mask
```
 pointer to the mask
 - dialog
```
MainDialog dialog
```
 pointer to the main bUnwarpJ dialog
 - hue
```
float hue
```
 hue for assigning new color ([0.0-1.0])
 - saturation
```
float saturation
```
 saturation for assigning new color ([0.5-1.0])
- Class bunwarpj.PointToolbar extends Canvas implements Serializable
 
 serialVersionUID:
 
 4280253125939921252L
 - Serialized Fields
 - down
```
boolean[] down
```
 flags for every tool
 - g
```
Graphics g
```
 graphic pointer
 - sourceImp
```
ij.ImagePlus sourceImp
```
 source image pointer
 - targetImp
```
ij.ImagePlus targetImp
```
 target image pointer
 - previousInstance
```
Toolbar previousInstance
```
 previous toolbar instance
 - sourcePh
```
PointHandler sourcePh
```
 source point handler
 - targetPh
```
PointHandler targetPh
```
 target point handler
 - instance
```
PointToolbar instance
```
 toolbar instance
 - mouseDownTime
```
long mouseDownTime
```
 mouse down time
 - currentTool
```
int currentTool
```
 current tool
 - x
```
int x
```
 x- coordinate
 - y
```
int y
```
 y- coordinate
 - xOffset
```
int xOffset
```
 x- offset
 - yOffset
```
int yOffset
```
 y- offset
 - dialog
```
MainDialog dialog
```
 pointer to the bUnwarpJ dialog
Package bunwarpj.trakem2.transform
- Class bunwarpj.trakem2.transform.CubicBSplineTransform extends AbstractModel<CubicBSplineTransform> implements Serializable
 - Serialized Fields
 - swx
```
BSplineModel swx
```
 grid of B-spline coefficients for x- transformation
 - swy
```
BSplineModel swy
```
 grid of B-spline coefficients for y- transformation
 - intervals
```
int intervals
```
 number of intervals between B-spline coefficients
 - width
```
int width
```
 width of the image to be transformed
 - height
```
int height
```
 height of the image to be transformed
 - sourceWidth
```
int sourceWidth
```
 width of the source image (necessary for the fit method)
 - sourceHeight
```
int sourceHeight
```
 height of the source image (necessary for the fit method)
 - parameter
```
Param parameter
```
 bUnwarpJ parameters (necessary for the fit method)
Package customnode
- Class customnode.FullInfoMesh.Vertex extends Point3f implements Serializable
 - Serialized Fields
 - edges
```
HashSet<E> edges
```
 - triangles
```
HashSet<E> triangles
```
Package edu.utexas.archipelago.image
- Class edu.utexas.archipelago.image.ImageBlockDeblock extends Object implements Serializable
 - Serialized Fields
 - inputFile
```
File inputFile
```
 Contains input file path
 - outputFile
```
File outputFile
```
 Contains output file path
 - blockFiles
```
ArrayList<E> blockFiles
```
 List of files containing image blocks.
 - boxMap
```
ArrayList<E> boxMap
```
 Corresponding list of bounding box maps. Each array is like [x0, y0, xb0, yb0, w, h], where the pixel at (x0, y0) in the combined image corresponds to the pixel at (xb0, yb0) in the block image. w and h represent the width and height of the valid window in the block image. This is at most the block size, but may be smaller, and excludes the overlap region.
 - blockSize
```
int[] blockSize
```
 Requested size of the block images.
 - halfOverlap
```
int[] halfOverlap
```
 Stores the overlap size, halved.
 - ovlpCorrection
```
int[] ovlpCorrection
```
 Since we divide the overlap in two and store as int[]. we also store a correction value which is zero if overlap is even and 1 if odd.
 - chunkMaps
```
ArrayList<E> chunkMaps
```
 Maps input block image files to output block image files.
 - n
```
int n
```
 - w
```
int w
```
 Width and height of the input image.
 - h
```
int h
```
 Width and height of the input image.
 - self
```
ImageBlockDeblock self
```
 - subfolder
```
String subfolder
```
Package edu.utexas.archipelago.segmentation
- Class edu.utexas.archipelago.segmentation.BatchWekaSegmentation.WekaSegmentationCallable extends Object implements Serializable
  - Serialized Fields
    - file
```
File file
```
    - classifier
```
File classifier
```
    - index
```
int index
```
Package edu.utexas.clm.archipelago.compute
- Class edu.utexas.clm.archipelago.compute.ProcessManager extends Object implements Serializable
 
 serialVersionUID:
 
 -5729538939085054236L
 - Serialized Fields
 - callable
```
Callable<V> callable
```
 - output
```
Object output
```
 - id
```
long id
```
 - remoteException
```
Throwable remoteException
```
 - runningOn
```
long runningOn
```
 - numCores
```
float numCores
```
 - isFractional
```
boolean isFractional
```
- Class edu.utexas.clm.archipelago.compute.QuickCallable extends Object implements Serializable
 
 serialVersionUID:
 
 8311164115029763772L
 - Serialized Fields
 - r
```
Runnable r
```
Package edu.utexas.clm.archipelago.data
- Class edu.utexas.clm.archipelago.data.ClusterMessage extends Object implements Serializable
 
 serialVersionUID:
 
 650327564966436764L
 - Serialized Fields
 - type
```
MessageType type
```
 - o
```
Serializable o
```
 - source
```
long source
```
- Class edu.utexas.clm.archipelago.data.DataChunk extends Object implements Serializable
 
 serialVersionUID:
 
 3307652134796685516L
 - Serialized Fields
 - lastOn
```
long lastOn
```
 - lastTime
```
long lastTime
```
 - id
```
long id
```
 - mark
```
int mark
```
- Class edu.utexas.clm.archipelago.data.Duplex extends Object implements Serializable
 - Serialized Fields
 - a
```
Object a
```
 - b
```
Object b
```
- Class edu.utexas.clm.archipelago.data.FileChunk extends DataChunk<String> implements Serializable
 
 serialVersionUID:
 
 -8641288090205214129L
 - Serialized Fields
 - fileName
```
String fileName
```
 - doAppend
```
boolean doAppend
```
- Class edu.utexas.clm.archipelago.data.HeartBeat extends Object implements Serializable
 
 serialVersionUID:
 
 -5771380117512667497L
 - Serialized Fields
 - ramMBAvailable
```
int ramMBAvailable
```
 - ramMBTotal
```
int ramMBTotal
```
 - ramMBMax
```
int ramMBMax
```
- Class edu.utexas.clm.archipelago.data.SimpleChunk extends DataChunk<T> implements Serializable
 - Serialized Fields
 - t
```
Object t
```
Package edu.utexas.clm.archipelago.example
- Class edu.utexas.clm.archipelago.example.Cluster_SIFT.SIFTCall extends Object implements Serializable
 - Serialized Fields
 - param
```
FloatArray2DSIFT.Param param
```
 - fileChunk
```
FileChunk fileChunk
```
- Class edu.utexas.clm.archipelago.example.Equality_Example.EqCall extends Object implements Serializable
 - Serialized Fields
 - floats
```
ArrayList<E> floats
```
- Class edu.utexas.clm.archipelago.example.Stress_Test.Stressor extends Object implements Serializable
 - Serialized Fields
 - stresses
```
int stresses
```
- Class edu.utexas.clm.archipelago.example.Test_Cluster.NullCall extends Object implements Serializable
 - Serialized Fields
 - winks
```
long winks
```
 - nc
```
int nc
```
 - string
```
String string
```
Package edu.utexas.clm.archipelago.exception
- Class edu.utexas.clm.archipelago.exception.AuthenticationException extends ShellExecutionException implements Serializable
- Class edu.utexas.clm.archipelago.exception.ShellExecutionException extends Exception implements Serializable
Package edu.utexas.clm.archipelago.ijsupport
- Class edu.utexas.clm.archipelago.ijsupport.AbstractAffineModelChunk extends DataChunk<AbstractAffineModel2D<?>> implements Serializable
- Class edu.utexas.clm.archipelago.ijsupport.FloatProcessorChunk extends DataChunk<ij.process.FloatProcessor> implements Serializable
 - Serialization Methods
 - readObject
```
private void readObject(ObjectInputStream ois)
 throws IOException,
 ClassNotFoundException
```
 Throws:
 
 IOException
 
 ClassNotFoundException
 - Serialized Fields
 - pixels
```
float[] pixels
```
 - width
```
int width
```
 - height
```
int height
```
Package edu.utexas.clm.archipelago.ijsupport.bottle
- Class edu.utexas.clm.archipelago.ijsupport.bottle.LayerBottle extends Object implements Serializable
  - Serialized Fields
    - id
```
long id
```
    - file
```
File file
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.LayerBottler extends Object implements Serializable
- Class edu.utexas.clm.archipelago.ijsupport.bottle.PatchBottle extends Object implements Serializable
  - Serialized Fields
    - projectFile
```
File projectFile
```
    - id
```
long id
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.PatchBottler extends Object implements Serializable
- Class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottle extends Object implements Serializable
  - Serialized Fields
    - w
```
double[] w
```
    - l
```
double[] l
```
    - id
```
long id
```
    - fromOrigin
```
boolean fromOrigin
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottle.IdPoint extends Point implements Serializable
  - Serialized Fields
    - id
```
long id
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottler extends Object implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
                        IOException
```
      Throws:
      
      ClassNotFoundException
      
      IOException
  - Serialized Fields
    - isOrigin
```
boolean isOrigin
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.SIFTParamBottle extends Object implements Serializable
  - Serialized Fields
    - fdSize
```
int fdSize
```
    - fdBins
```
int fdBins
```
    - maxOctaveSize
```
int maxOctaveSize
```
    - minOctaveSize
```
int minOctaveSize
```
    - steps
```
int steps
```
    - initialSigma
```
float initialSigma
```
    - maxEpsilon
```
float maxEpsilon
```
    - minInlierRatio
```
float minInlierRatio
```
    - minNumInliers
```
int minNumInliers
```
    - expectedModelIndex
```
int expectedModelIndex
```
    - multipleHypotheses
```
boolean multipleHypotheses
```
    - widestSetOnly
```
boolean widestSetOnly
```
    - rejectIdentity
```
boolean rejectIdentity
```
    - identityTolerance
```
float identityTolerance
```
    - maxNumNeighbors
```
int maxNumNeighbors
```
    - maxNumFailures
```
int maxNumFailures
```
    - desiredModelIndex
```
int desiredModelIndex
```
    - maxIterationsOptimize
```
int maxIterationsOptimize
```
    - maxPlateauwidthOptimize
```
int maxPlateauwidthOptimize
```
    - visualize
```
boolean visualize
```
    - maxNumThreads
```
int maxNumThreads
```
    - regularize
```
boolean regularize
```
    - regularizerIndex
```
int regularizerIndex
```
    - lambda
```
double lambda
```
    - rod
```
float rod
```
    - clearCache
```
boolean clearCache
```
    - maxNumThreadsSift
```
int maxNumThreadsSift
```
- Class edu.utexas.clm.archipelago.ijsupport.bottle.SIFTParamBottler extends Object implements Serializable
Package edu.utexas.clm.archipelago.network.translation
- Class edu.utexas.clm.archipelago.network.translation.FileBottle extends Object implements Serializable
  - Serialized Fields
    - path
```
String path
```
    - exists
```
boolean exists
```
- Class edu.utexas.clm.archipelago.network.translation.FileBottler extends Object implements Serializable
Package edu.utexas.clm.archipelago.ui
- Class edu.utexas.clm.archipelago.ui.NodeConfigurationUI extends Panel implements Serializable
 - Serialized Fields
 - paramFactory
```
NodeParametersFactory paramFactory
```
 - nodePanels
```
Vector<E> nodePanels
```
 - removedNodes
```
Vector<E> removedNodes
```
 - centralPanel
```
Panel centralPanel
```
Package features
- Class features.SigmaPalette.PaletteCanvas extends ImageCanvas implements Serializable
  - Serialized Fields
    - owner
```
SigmaPalette owner
```
    - croppedWidth
```
int croppedWidth
```
    - croppedHeight
```
int croppedHeight
```
    - sigmasAcross
```
int sigmasAcross
```
    - sigmasDown
```
int sigmasDown
```
    - backBufferWidth
```
int backBufferWidth
```
    - backBufferHeight
```
int backBufferHeight
```
    - backBufferGraphics
```
Graphics backBufferGraphics
```
    - backBufferImage
```
Image backBufferImage
```
- Class features.SigmaPalette.PaletteStackWindow extends StackWindow implements Serializable
  - Serialized Fields
    - owner
```
SigmaPalette owner
```
    - label
```
Label label
```
    - maxValueScrollbar
```
Scrollbar maxValueScrollbar
```
    - manuallyChangedAlready
```
boolean manuallyChangedAlready
```
Package fiji.debugging
- Class fiji.debugging.Object_Inspector.ObjectWrapper extends DefaultMutableTreeNode implements Serializable
  - Serialized Fields
    - title
```
String title
```
    - initialized
```
boolean initialized
```
Package fiji.plugin.timelapsedisplay
- Class fiji.plugin.timelapsedisplay.FileOpenMenuEntry extends AbstractAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - data
```
ArrayList<E> data
```
 - chartPanel
```
ChartPanel chartPanel
```
- Class fiji.plugin.timelapsedisplay.GraphFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - chart
```
JFreeChart chart
```
 - chartPanel
```
ChartPanel chartPanel
```
 - mouseListener
```
MouseListenerTimelapse mouseListener
```
 - mainPanel
```
JPanel mainPanel
```
 - referenceTimePoint
```
int referenceTimePoint
```
 - enableReferenceTimePoint
```
boolean enableReferenceTimePoint
```
Package fiji.plugin.trackmate
- Class fiji.plugin.trackmate.ModelChangeEvent extends EventObject implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - spots
```
HashSet<E> spots
```
 Spots affected by this event.
 - edges
```
HashSet<E> edges
```
 Edges affected by this event.
 - fromFrame
```
HashMap<K,V> fromFrame
```
 For spots removed or moved: frame from which they were removed or moved.
 - toFrame
```
HashMap<K,V> toFrame
```
 For spots removed or added: frame to which they were added or moved.
 - spotFlags
```
HashMap<K,V> spotFlags
```
 Modification flag for spots affected by this event.
 - edgeFlags
```
HashMap<K,V> edgeFlags
```
 Modification flag for edges affected by this event.
 - eventID
```
int eventID
```
 The event type for this instance.
 - trackUpdated
```
Set<E> trackUpdated
```
- Class fiji.plugin.trackmate.SelectionChangeEvent extends EventObject implements Serializable
 
 serialVersionUID:
 
 -8920831578922412606L
 - Serialized Fields
 - edges
```
Map<K,V> edges
```
 Changes in DefaultWeightedEdge selection this event represents.
 - spots
```
Map<K,V> spots
```
 Changes in Spot selection this event represents.
Package fiji.plugin.trackmate.action
- Class fiji.plugin.trackmate.action.CaptureOverlayPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - firstFrame
```
int firstFrame
```
    - lastFrame
```
int lastFrame
```
    - hideImage
```
boolean hideImage
```
- Class fiji.plugin.trackmate.action.LabelImgExporterPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - exportSpotsAsDots
```
JCheckBox exportSpotsAsDots
```
    - exportTracksOnly
```
JCheckBox exportTracksOnly
```
Package fiji.plugin.trackmate.features
- Class fiji.plugin.trackmate.features.EdgeCollectionDataset extends ModelDataset implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - edges
```
List<E> edges
```
 - edgeColorGenerator
```
FeatureColorGenerator<K> edgeColorGenerator
```
 - edgeMap
```
Map<K,V> edgeMap
```
 - labelGenerator
```
Function<T,R> labelGenerator
```
- Class fiji.plugin.trackmate.features.ModelDataset extends AbstractDataset implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
Model model
```
 - yFeatures
```
List<E> yFeatures
```
 - xFeature
```
String xFeature
```
 - ds
```
DisplaySettings ds
```
 - selectionModel
```
SelectionModel selectionModel
```
 - stroke
```
BasicStroke stroke
```
 - selectionStroke
```
BasicStroke selectionStroke
```
 - featureNameMap
```
Map<K,V> featureNameMap
```
- Class fiji.plugin.trackmate.features.SpotCollectionDataset extends ModelDataset implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - spots
```
List<E> spots
```
 - spotColorGenerator
```
FeatureColorGenerator<K> spotColorGenerator
```
 - edgeMap
```
Map<K,V> edgeMap
```
- Class fiji.plugin.trackmate.features.TrackCollectionDataset extends ModelDataset implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - trackIDs
```
List<E> trackIDs
```
 - trackColorGenerator
```
FeatureColorGenerator<K> trackColorGenerator
```
Package fiji.plugin.trackmate.gui.components
- Class fiji.plugin.trackmate.gui.components.ActionChooserPanel extends ModuleChooserPanel<TrackMateActionFactory> implements Serializable
 
 serialVersionUID:
 
 1L
- Class fiji.plugin.trackmate.gui.components.CategoryJComboBox extends JComboBox<Object> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - categoryIndexSet
```
HashSet<E> categoryIndexSet
```
 Indices of items that should be displayed as a category name.
 - isCategoryIndex
```
boolean isCategoryIndex
```
 - itemNames
```
Map<K,V> itemNames
```
 - invertMap
```
HashMap<K,V> invertMap
```
 - categoryNames
```
Map<K,V> categoryNames
```
- Class fiji.plugin.trackmate.gui.components.ConfigurationPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - PREVIEW_BUTTON_PUSHED
```
ActionEvent PREVIEW_BUTTON_PUSHED
```
 This event is fired when a preview button is fired within this configuration panel. It is the responsibility of concrete implementation to do whatever they want with it.
- Class fiji.plugin.trackmate.gui.components.ConfigureViewsPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
- Class fiji.plugin.trackmate.gui.components.FeaturePlotSelectionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - panelYFeatures
```
JPanel panelYFeatures
```
 - cmbboxXFeature
```
JComboBox<E> cmbboxXFeature
```
 - comboBoxes
```
Stack<E> comboBoxes
```
 - struts
```
Stack<E> struts
```
 - features
```
List<E> features
```
 - featureNames
```
Map<K,V> featureNames
```
- Class fiji.plugin.trackmate.gui.components.FilterGuiPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - CHANGE_EVENT
```
ChangeEvent CHANGE_EVENT
```
 - COLOR_FEATURE_CHANGED
```
ActionEvent COLOR_FEATURE_CHANGED
```
 - updater
```
OnRequestUpdater updater
```
 - filterPanels
```
Stack<E> filterPanels
```
 - struts
```
Stack<E> struts
```
 - featureFilters
```
List<E> featureFilters
```
 - changeListeners
```
List<E> changeListeners
```
 - model
```
Model model
```
 - allThresholdsPanel
```
JPanel allThresholdsPanel
```
 - lblInfo
```
JLabel lblInfo
```
 - target
```
DisplaySettings.TrackMateObject target
```
 - settings
```
Settings settings
```
 - defaultFeature
```
String defaultFeature
```
 - logger
```
fiji.plugin.trackmate.gui.components.FilterGuiPanel.ProgressBarLogger logger
```
 - lblTop
```
JLabel lblTop
```
 - progressBar
```
JProgressBar progressBar
```
- Class fiji.plugin.trackmate.gui.components.FilterPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - CHANGE_EVENT
```
ChangeEvent CHANGE_EVENT
```
 - plot
```
XYPlot plot
```
 - intervalMarker
```
IntervalMarker intervalMarker
```
 - threshold
```
double threshold
```
 - valueCollector
```
Function<T,R> valueCollector
```
 - annotation
```
XYTextSimpleAnnotation annotation
```
 - listeners
```
ArrayList<E> listeners
```
 - rdbtnAbove
```
JRadioButton rdbtnAbove
```
 - rdbtnBelow
```
JRadioButton rdbtnBelow
```
 - cmbboxFeatureKeys
```
JComboBox<E> cmbboxFeatureKeys
```
- Class fiji.plugin.trackmate.gui.components.GrapherPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - trackmate
```
TrackMate trackmate
```
 - panelSpot
```
JPanel panelSpot
```
 - panelEdges
```
JPanel panelEdges
```
 - panelTracks
```
JPanel panelTracks
```
 - spotFeatureSelectionPanel
```
FeaturePlotSelectionPanel spotFeatureSelectionPanel
```
 - edgeFeatureSelectionPanel
```
FeaturePlotSelectionPanel edgeFeatureSelectionPanel
```
 - trackFeatureSelectionPanel
```
FeaturePlotSelectionPanel trackFeatureSelectionPanel
```
 - displaySettings
```
DisplaySettings displaySettings
```
 - selectionModel
```
SelectionModel selectionModel
```
 - panelSelection
```
JPanel panelSelection
```
 - rdbtnAll
```
JRadioButton rdbtnAll
```
 - rdbtnSelection
```
JRadioButton rdbtnSelection
```
 - rdbtnTracks
```
JRadioButton rdbtnTracks
```
- Class fiji.plugin.trackmate.gui.components.InitFilterPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - updater
```
OnRequestUpdater updater
```
 - valueCollector
```
Function<T,R> valueCollector
```
 - filterPanel
```
FilterPanel filterPanel
```
 - lblSelectedSpots
```
JLabel lblSelectedSpots
```
 - values
```
double[] values
```
- Class fiji.plugin.trackmate.gui.components.LogHistogramDataset extends HistogramDataset implements Serializable
 
 serialVersionUID:
 
 6012084169414194555L
- Class fiji.plugin.trackmate.gui.components.LogPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - textPane
```
JTextPane textPane
```
 - logger
```
Logger logger
```
- Class fiji.plugin.trackmate.gui.components.ModuleChooserPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - provider
```
AbstractProvider<K extends TrackMateModule> provider
```
 - cmbbox
```
JComboBox<E> cmbbox
```
- Class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation extends AbstractXYAnnotation implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - x
```
float x
```
 - y
```
float y
```
 - text
```
String text
```
 - font
```
Font font
```
 - color
```
Color color
```
 - chartPanel
```
ChartPanel chartPanel
```
Package fiji.plugin.trackmate.gui.components.detector
- Class fiji.plugin.trackmate.gui.components.detector.DogDetectorConfigurationPanel extends LogDetectorConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
- Class fiji.plugin.trackmate.gui.components.detector.LabelImageDetectorConfigurationPanel extends ThresholdDetectorConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
- Class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel extends ConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ftfQualityThreshold
```
JFormattedTextField ftfQualityThreshold
```
    - jCheckBoxMedianFilter
```
JCheckBox jCheckBoxMedianFilter
```
    - ftfDiameter
```
JFormattedTextField ftfDiameter
```
    - jCheckSubPixel
```
JCheckBox jCheckSubPixel
```
    - sliderChannel
```
JSlider sliderChannel
```
    - imp
```
ij.ImagePlus imp
```
- Class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel extends ConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ftfDiameter
```
JFormattedTextField ftfDiameter
```
- Class fiji.plugin.trackmate.gui.components.detector.MaskDetectorConfigurationPanel extends ThresholdDetectorConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
- Class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel extends ConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - settings
```
Settings settings
```
    - chkboxSimplify
```
JCheckBox chkboxSimplify
```
    - sliderChannel
```
JSlider sliderChannel
```
    - ftfIntensityThreshold
```
JFormattedTextField ftfIntensityThreshold
```
    - btnAutoThreshold
```
JButton btnAutoThreshold
```
    - lblIntensityThreshold
```
JLabel lblIntensityThreshold
```
Package fiji.plugin.trackmate.gui.components.tracker
- Class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - cmbboxFeature
```
JComboBox<E> cmbboxFeature
```
 - txtfldFeatureWeight
```
JFormattedTextField txtfldFeatureWeight
```
 - features
```
List<E> features
```
- Class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - panelButtons
```
JPanel panelButtons
```
 - btnRemove
```
JButton btnRemove
```
 - btnAdd
```
JButton btnAdd
```
 - featurePanels
```
Stack<E> featurePanels
```
 - features
```
List<E> features
```
 - featureNames
```
Map<K,V> featureNames
```
 - index
```
int index
```
- Class fiji.plugin.trackmate.gui.components.tracker.JPanelTrackerSettingsMain extends JPanel implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - lblSplittingMaxDistanceUnit
```
JLabel lblSplittingMaxDistanceUnit
```
 - txtfldSplittingMaxDistance
```
JFormattedTextField txtfldSplittingMaxDistance
```
 - chkboxAllowSplitting
```
JCheckBox chkboxAllowSplitting
```
 - panelGapClosing
```
JPanelFeatureSelectionGui panelGapClosing
```
 - panelMergingFeatures
```
JPanelFeatureSelectionGui panelMergingFeatures
```
 - panelLinkingFeatures
```
JPanelFeatureSelectionGui panelLinkingFeatures
```
 - panelSplittingFeatures
```
JPanelFeatureSelectionGui panelSplittingFeatures
```
 - scrpneMergingFeatures
```
JScrollPane scrpneMergingFeatures
```
 - lblMergingMaxDistanceUnit
```
JLabel lblMergingMaxDistanceUnit
```
 - txtfldMergingMaxDistance
```
JFormattedTextField txtfldMergingMaxDistance
```
 - chkboxAllowMerging
```
JCheckBox chkboxAllowMerging
```
 - scrpneSplittingFeatures
```
JScrollPane scrpneSplittingFeatures
```
 - scrpneGapClosingFeatures
```
JScrollPane scrpneGapClosingFeatures
```
 - txtfldGapClosingMaxFrameInterval
```
JFormattedTextField txtfldGapClosingMaxFrameInterval
```
 - lblGapClosingMaxDistanceUnit
```
JLabel lblGapClosingMaxDistanceUnit
```
 - txtfldGapClosingMaxDistance
```
JFormattedTextField txtfldGapClosingMaxDistance
```
 - chkboxAllowGapClosing
```
JCheckBox chkboxAllowGapClosing
```
 - lblLinkingMaxDistanceUnits
```
JLabel lblLinkingMaxDistanceUnits
```
 - txtfldLinkingMaxDistance
```
JFormattedTextField txtfldLinkingMaxDistance
```
 - lbl6
```
JLabel lbl6
```
 - lbl7
```
JLabel lbl7
```
 - lbl8
```
JLabel lbl8
```
 - lbl10
```
JLabel lbl10
```
 - lbl15
```
JLabel lbl15
```
 - lbl13
```
JLabel lbl13
```
 - lbl16
```
JLabel lbl16
```
- Class fiji.plugin.trackmate.gui.components.tracker.KalmanTrackerConfigPanel extends ConfigurationPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - tfInitSearchRadius
```
JFormattedTextField tfInitSearchRadius
```
 - tfSearchRadius
```
JFormattedTextField tfSearchRadius
```
 - tfMaxFrameGap
```
JFormattedTextField tfMaxFrameGap
```
- Class fiji.plugin.trackmate.gui.components.tracker.LAPTrackerSettingsPanel extends ConfigurationPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - jPanelMain
```
JPanelTrackerSettingsMain jPanelMain
```
 - trackerName
```
String trackerName
```
 - spaceUnits
```
String spaceUnits
```
 - features
```
Collection<E> features
```
 - featureNames
```
Map<K,V> featureNames
```
- Class fiji.plugin.trackmate.gui.components.tracker.NearestNeighborTrackerSettingsPanel extends ConfigurationPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - maxDistField
```
JFormattedTextField maxDistField
```
 - labelTrackerDescription
```
JLabel labelTrackerDescription
```
 - labelUnits
```
JLabel labelUnits
```
 - labelTracker
```
JLabel labelTracker
```
 - infoText
```
String infoText
```
 - trackerName
```
String trackerName
```
 - spaceUnits
```
String spaceUnits
```
- Class fiji.plugin.trackmate.gui.components.tracker.SimpleLAPTrackerSettingsPanel extends ConfigurationPanel implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - txtfldGapClosingTimeCutoff
```
JFormattedTextField txtfldGapClosingTimeCutoff
```
 - txtfldGapClosingDistanceCutoff
```
JFormattedTextField txtfldGapClosingDistanceCutoff
```
 - txtfldLinkingDistance
```
JFormattedTextField txtfldLinkingDistance
```
Package fiji.plugin.trackmate.gui.displaysettings
- Class fiji.plugin.trackmate.gui.displaysettings.Colormap extends Object implements Serializable
 
 serialVersionUID:
 
 2977884191627862512L
 - Serialized Fields
 - lowerBound
```
double lowerBound
```
 - upperBound
```
double upperBound
```
 - colors
```
TreeMap<K,V> colors
```
 - defaultColor
```
Color defaultColor
```
 - name
```
String name
```
- Class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - colorChooser
```
JColorChooser colorChooser
```
 - styleElements
```
List<E> styleElements
```
- Class fiji.plugin.trackmate.gui.displaysettings.SliderPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 6444334522127424416L
 - Serialized Fields
 - slider
```
JSlider slider
```
 - spinner
```
JSpinner spinner
```
 - model
```
BoundedValue model
```
- Class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble extends JPanel implements Serializable
 
 serialVersionUID:
 
 6444334522127424416L
 - Serialized Fields
 - slider
```
JSlider slider
```
 - spinner
```
JSpinner spinner
```
 - model
```
BoundedValueDouble model
```
 - dmin
```
double dmin
```
 - dmax
```
double dmax
```
 - userDefinedNumberFormat
```
boolean userDefinedNumberFormat
```
 - rangeListener
```
SliderPanelDouble.RangeListener rangeListener
```

Package fiji.plugin.trackmate.gui.wizard

Class fiji.plugin.trackmate.gui.wizard.WizardPanel extends JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

cardLayout
```
CardLayout cardLayout
```

animatorPanel

fiji.plugin.trackmate.gui.wizard.WizardPanel.AnimatorPanel animatorPanel

panelMain
```
JPanel panelMain
```
btnSave
```
JButton btnSave
```
btnLog
```
JToggleButton btnLog
```
btnDisplayConfig
```
JToggleButton btnDisplayConfig
```
btnPrevious
```
JButton btnPrevious
```
btnNext
```
JButton btnNext
```
btnCancel
```
JButton btnCancel
```
btnResume
```
JButton btnResume
```
panelButtons
```
JPanel panelButtons
```

Package fiji.plugin.trackmate.tracking.overlap
- Class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerSettingsPanel extends ConfigurationPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ftfScaleFactor
```
JFormattedTextField ftfScaleFactor
```
    - ftfMinIoU
```
JFormattedTextField ftfMinIoU
```
    - rdbtnFast
```
JRadioButton rdbtnFast
```
    - rdbtnPrecise
```
JRadioButton rdbtnPrecise
```
Package fiji.plugin.trackmate.util
- Class fiji.plugin.trackmate.util.ExportableChartPanel extends ChartPanel implements Serializable
 
 serialVersionUID:
 
 1L
- Class fiji.plugin.trackmate.util.ExportableChartValueTable extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - table
```
TablePanel<O> table
```
- Class fiji.plugin.trackmate.util.JLabelLogger extends JLabel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - logger
```
fiji.plugin.trackmate.util.JLabelLogger.MyLogger logger
```
Package fiji.plugin.trackmate.visualization.hyperstack
- Class fiji.plugin.trackmate.visualization.hyperstack.SpotEditToolConfigPanel extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - logger
```
Logger logger
```
 - jNFQualityThreshold
```
JFormattedTextField jNFQualityThreshold
```
 - jNFDistanceTolerance
```
JFormattedTextField jNFDistanceTolerance
```
 - jNFNFrames
```
JFormattedTextField jNFNFrames
```
 - parent
```
SpotEditTool parent
```
 - jNFNStepwiseTime
```
JFormattedTextField jNFNStepwiseTime
```
- Class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay extends Roi implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - editingSpot
```
Spot editingSpot
```
 - calibration
```
double[] calibration
```
 - fm
```
FontMetrics fm
```
 - spotSelection
```
Collection<E> spotSelection
```
 - displaySettings
```
DisplaySettings displaySettings
```
 - model
```
Model model
```
- Class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay extends Roi implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - calibration
```
double[] calibration
```
 - highlight
```
Collection<E> highlight
```
 - displaySettings
```
DisplaySettings displaySettings
```
 - model
```
Model model
```
Package fiji.plugin.trackmate.visualization.table
- Class fiji.plugin.trackmate.visualization.table.AllSpotsTableView extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
Model model
```
 - spotTable
```
TablePanel<O> spotTable
```
 - ignoreSelectionChange
```
AtomicBoolean ignoreSelectionChange
```
 - selectionModel
```
SelectionModel selectionModel
```
- Class fiji.plugin.trackmate.visualization.table.BranchTableView extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
Model model
```
 - branchTable
```
TablePanel<O> branchTable
```
- Class fiji.plugin.trackmate.visualization.table.TrackTableView extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - model
```
Model model
```
 - spotTable
```
TablePanel<O> spotTable
```
 - edgeTable
```
TablePanel<O> edgeTable
```
 - trackTable
```
TablePanel<O> trackTable
```
 - ignoreSelectionChange
```
AtomicBoolean ignoreSelectionChange
```
 - selectionModel
```
SelectionModel selectionModel
```
Package fiji.plugin.trackmate.visualization.trackscheme
- Class fiji.plugin.trackmate.visualization.trackscheme.InfoPane extends JPanel implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - table
```
JTable table
```
 - scrollTable
```
JScrollPane scrollTable
```
 - doHighlightSelection
```
boolean doHighlightSelection
```
 - model
```
Model model
```
 - selectionModel
```
SelectionModel selectionModel
```
 - spotSelection
```
Collection<E> spotSelection
```
 A copy of the last spot collection highlighted in this infopane, sorted by frame order.
 - updater
```
OnRequestUpdater updater
```
 - headers
```
String[] headers
```
 The table headers, taken from spot feature names.
- Class fiji.plugin.trackmate.visualization.trackscheme.SaveAction extends AbstractAction implements Serializable
 
 serialVersionUID:
 
 7672151690754466760L
 - Serialized Fields
 - lastDir
```
String lastDir
```
 - trackScheme
```
TrackScheme trackScheme
```
- Class fiji.plugin.trackmate.visualization.trackscheme.SmallFeaturePlotSelectionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - panelYFeatures
```
JPanel panelYFeatures
```
 - comboBoxes
```
Stack<E> comboBoxes
```
 - struts
```
Stack<E> struts
```
 - features
```
List<E> features
```
 - featureNames
```
Map<K,V> featureNames
```
- Class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions.EditAction extends AbstractAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - graphComponent
```
TrackSchemeGraphComponent graphComponent
```
- Class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - infoPane
```
InfoPane infoPane
```
 The side pane in which spot selection info will be displayed.
 - graph
```
JGraphXAdapter graph
```
 - trackScheme
```
TrackScheme trackScheme
```
 - graphComponent
```
TrackSchemeGraphComponent graphComponent
```
 The graph component in charge of painting the graph.
 - logger
```
Logger logger
```
 - displaySettings
```
DisplaySettings displaySettings
```
- Class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent extends com.mxgraph.swing.mxGraphComponent implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - columnWidths
```
int[] columnWidths
```
 The width of the columns for each track, from left to right.
 - columnTrackIDs
```
Integer[] columnTrackIDs
```
 The trackID for each column.
 - trackScheme
```
TrackScheme trackScheme
```
 - paintDecorationLevel
```
int paintDecorationLevel
```
 - spaceDown
```
boolean spaceDown
```
 Flag that states whether the use is holding the space key down.
 - ds
```
DisplaySettings ds
```
- Class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemePopupMenu extends JPopupMenu implements Serializable
 
 serialVersionUID:
 
 -1L
 - Serialized Fields
 - cell
```
Object cell
```
 The cell where the right-click was made, null if the right-click is made out of a cell.
 - trackScheme
```
TrackScheme trackScheme
```
 The TrackScheme instance.
 - point
```
Point point
```
 The right-click location.
- Class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeToolbar extends JToolBar implements Serializable
 
 serialVersionUID:
 
 3442140463984241266L
 - Serialized Fields
 - trackScheme
```
TrackScheme trackScheme
```
Package fiji.plugin.trackmate.visualization.trackscheme.utils
- Class fiji.plugin.trackmate.visualization.trackscheme.utils.SearchBar extends JTextField implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - observer
```
PropertyChangeSupport observer
```
    - model
```
Model model
```
    - view
```
TrackMateModelView view
```

Package fiji.plugin.volumeviewer

Class fiji.plugin.volumeviewer.Gradient extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - height
```
int height
```
  - width
```
int width
```
  - wA
```
int wA
```
  - control
```
Control control
```
  - lut
```
int[][] lut
```
  - vv
```
Volume_Viewer vv
```

Class fiji.plugin.volumeviewer.Gui extends JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

upperButtonPanel
```
JPanel upperButtonPanel
```
lowerButtonPanel
```
JPanel lowerButtonPanel
```
transferFunctionPanel
```
JPanel transferFunctionPanel
```
centerPanel
```
JPanel centerPanel
```
slicePanel
```
JPanel slicePanel
```
checkSlices
```
JCheckBox checkSlices
```
checkAxes
```
JCheckBox checkAxes
```
checkClipLines
```
JCheckBox checkClipLines
```
renderChoice
```
JComboBox<E> renderChoice
```
interpolationChoice
```
JComboBox<E> interpolationChoice
```
lutChoice
```
JComboBox<E> lutChoice
```
checkPickColor2
```
JCheckBox checkPickColor2
```
checkPickColor3
```
JCheckBox checkPickColor3
```
scaleSlider
```
JSlider scaleSlider
```
distSlider
```
JSlider distSlider
```
positionXSlider
```
JSlider positionXSlider
```
positionYSlider
```
JSlider positionYSlider
```
positionZSlider
```
JSlider positionZSlider
```
scaleSliderValue
```
float scaleSliderValue
```
zAspectLabel
```
JLabel zAspectLabel
```
zAspectString
```
String zAspectString
```
tfZaspect
```
JTextField tfZaspect
```
samplingLabel
```
JLabel samplingLabel
```
samplingString
```
String samplingString
```
tfSampling
```
JTextField tfSampling
```
xStart
```
int xStart
```
yStart
```
int yStart
```
xAct
```
int xAct
```
yAct
```
int yAct
```
scaleLabel1
```
JLabel scaleLabel1
```
scaleLabel2
```
JLabel scaleLabel2
```
distLabel1
```
JLabel distLabel1
```
distLabel2
```
JLabel distLabel2
```
positionLabel
```
JLabel positionLabel
```
valueLabel
```
JLabel valueLabel
```

imageRegion

fiji.plugin.volumeviewer.ImageRegion imageRegion

sliceImageRegion

fiji.plugin.volumeviewer.ImageRegion sliceImageRegion

spinnerX
```
JSpinner spinnerX
```
spinnerY
```
JSpinner spinnerY
```
spinnerZ
```
JSpinner spinnerZ
```
enableSpinnerChangeListener
```
boolean enableSpinnerChangeListener
```
alphaSlider1
```
JSlider alphaSlider1
```
alphaSlider2
```
JSlider alphaSlider2
```
alphaSlider3
```
JSlider alphaSlider3
```
alphaSlider4
```
JSlider alphaSlider4
```
sliderLumTolerance
```
JSlider sliderLumTolerance
```
sliderGradTolerance
```
JSlider sliderGradTolerance
```
autobutton1
```
JButton autobutton1
```
autobutton2
```
JButton autobutton2
```
autobutton3
```
JButton autobutton3
```
clearbutton1
```
JButton clearbutton1
```
clearbutton2
```
JButton clearbutton2
```
clearbutton3
```
JButton clearbutton3
```
clearbutton4
```
JButton clearbutton4
```
transferFunctionTabbedPane
```
JTabbedPane transferFunctionTabbedPane
```
lightBox
```
JPanel lightBox
```
positionString
```
String positionString
```
valueString
```
String valueString
```
positionX
```
int positionX
```
positionY
```
int positionY
```
positionZ
```
int positionZ
```
maxPositionX
```
int maxPositionX
```
maxPositionY
```
int maxPositionY
```
maxPositionZ
```
int maxPositionZ
```
pic
```
Pic pic
```
picSlice
```
Pic picSlice
```
control
```
Control control
```
vv
```
Volume_Viewer vv
```
checkLight
```
JCheckBox checkLight
```
ambientSlider
```
JSlider ambientSlider
```
diffuseSlider
```
JSlider diffuseSlider
```
specularSlider
```
JSlider specularSlider
```
shineSlider
```
JSlider shineSlider
```

imageLightRegion

fiji.plugin.volumeviewer.ImageRegion imageLightRegion

picLight
```
Pic picLight
```

imageLEDRegion

fiji.plugin.volumeviewer.ImageRegion imageLEDRegion

picLED
```
Pic picLED
```
jLabelLight
```
JLabel jLabelLight
```
objectLightSlider
```
JSlider objectLightSlider
```
startR
```
long startR
```

Class fiji.plugin.volumeviewer.TFalpha1 extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - height
```
int height
```
  - width
```
int width
```
  - pixels
```
int[] pixels
```
  - sampleValue
```
int sampleValue
```
  - control
```
Control control
```
  - vol
```
Volume vol
```
  - alpha1
```
float[] alpha1
```
  - a1
```
int[] a1
```
  - alphaOffset
```
int alphaOffset
```
  - xLast
```
int xLast
```
  - yLast
```
int yLast
```
  - count
```
int count
```
Class fiji.plugin.volumeviewer.TFalpha2 extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - height
```
int height
```
  - width
```
int width
```
  - alpha2back
```
int[][] alpha2back
```
  - alpha2
```
float[][] alpha2
```
  - a2
```
int[][] a2
```
  - scaleAlpha
```
int scaleAlpha
```
  - pixels
```
int[] pixels
```
  - sampleValue
```
int sampleValue
```
  - gradValue
```
int gradValue
```
  - control
```
Control control
```
  - vol
```
Volume vol
```
  - lut2D_2
```
int[][][] lut2D_2
```
  - lut
```
int[][] lut
```
  - xLast
```
int xLast
```
  - yLast
```
int yLast
```
  - count
```
int count
```
Class fiji.plugin.volumeviewer.TFalpha3 extends JPanel implements Serializable

serialVersionUID:

-1L
- Serialized Fields
  - height
```
int height
```
  - width
```
int width
```
  - pixels
```
int[] pixels
```
  - sampleMean
```
int sampleMean
```
  - sampleDiff
```
int sampleDiff
```
  - control
```
Control control
```
  - vol
```
Volume vol
```
  - lut
```
int[][] lut
```
  - alpha3back
```
int[][] alpha3back
```
  - alpha3
```
int[][] alpha3
```
  - a3
```
int[][] a3
```
  - scaleAlpha
```
int scaleAlpha
```
  - lut2D_3
```
int[][][] lut2D_3
```
  - count
```
int count
```
Class fiji.plugin.volumeviewer.TFalpha4 extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - control
```
Control control
```
  - widthV
```
int widthV
```
  - heightV
```
int heightV
```
  - depthV
```
int depthV
```
  - alpha_3D
```
byte[][][] alpha_3D
```
  - aPaint_3D2
```
byte[][][] aPaint_3D2
```
  - alphaOffset
```
int alphaOffset
```
  - xLast
```
int xLast
```
  - yLast
```
int yLast
```
  - count
```
int count
```
Class fiji.plugin.volumeviewer.TFrgb extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - height
```
int height
```
  - channel
```
int channel
```
  - control
```
Control control
```
  - vv
```
Volume_Viewer vv
```
  - xLast
```
int xLast
```
  - yLast
```
int yLast
```
  - count
```
int count
```

Package fiji.process
- Class fiji.process.IepGui extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - n_image_box
```
int n_image_box
```
 Number of image boxes currently displayed
 - images
```
ArrayList<E> images
```
 List of ImagePlus currently opened in ImageJ
 - image_names
```
String[] image_names
```
 Array of images names, for display in image boxes
 - labels
```
ArrayList<E> labels
```
 List of Labels for the image boxes
 - image_boxes
```
ArrayList<E> image_boxes
```
 List of Combo boxes
 - variables
```
String[] variables
```
 Array of image variables
 - expression_history
```
DefaultComboBoxModel<E> expression_history
```
 This is where we store the history of valid command.
 - image_expression_parser
```
Image_Expression_Parser<T extends RealType<T> & NativeType<T>> image_expression_parser
```
 The plugin that normally calls this GUI and is responsible for calculations. If null, it will be instantiated.
 - target_imp
```
ij.ImagePlus target_imp
```
 The ImagePlus that will be used to display results.
 - jPanelImages
```
JPanel jPanelImages
```
 - jSplitPane1
```
JSplitPane jSplitPane1
```
 - jButtonMinus
```
JButton jButtonMinus
```
 - jButtonPlus
```
JButton jButtonPlus
```
 - jPanelLeftButtons
```
JPanel jPanelLeftButtons
```
 - jScrollPaneImages
```
JScrollPane jScrollPaneImages
```
 - jPanelLeft
```
JPanel jPanelLeft
```
 - jPanelRight
```
JPanel jPanelRight
```
 - jTextAreaInfo
```
JEditorPane jTextAreaInfo
```
 - jScrollPane1
```
JScrollPane jScrollPane1
```
 - jButtonOK
```
JButton jButtonOK
```
 - jButtonCancel
```
JButton jButtonCancel
```
 - expressionField
```
JComboBox<E> expressionField
```
 - jLabelExpression
```
JLabel jLabelExpression
```
Package fiji.util
- Class fiji.util.ArrowOptionPanel extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - listenerList
```
EventListenerList listenerList
```
 A list of event listeners for this component.
 - firingActionEvent
```
boolean firingActionEvent
```
 - jPanelMain
```
JPanel jPanelMain
```
 - jLabelArrowThickness
```
JLabel jLabelArrowThickness
```
 - jSliderArrowThickness
```
JSlider jSliderArrowThickness
```
 - canvasDrawingArea
```
Canvas canvasDrawingArea
```
 - jPanelDrawArea
```
JPanel jPanelDrawArea
```
 - jCheckBoxFillArrow
```
JCheckBox jCheckBoxFillArrow
```
 - jTextFieldArrowThickness
```
JTextField jTextFieldArrowThickness
```
 - jLabelArrowLength
```
JLabel jLabelArrowLength
```
 - jTextFieldHeadLength
```
JTextField jTextFieldHeadLength
```
 - jSliderHeadLength
```
JSlider jSliderHeadLength
```
 - jComboBoxHeadStyle
```
JComboBox<E> jComboBoxHeadStyle
```
 - jLabelHeadStyle
```
JLabel jLabelHeadStyle
```
Package fiji.util.gui
- Class fiji.util.gui.CommandFinderBase extends JFrame implements Serializable
 - Serialized Fields
 - prompt
```
JTextField prompt
```
 - completions
```
JList<E> completions
```
 - scrollPane
```
JScrollPane scrollPane
```
 - completionsModel
```
DefaultListModel<E> completionsModel
```
 - runButton
```
JButton runButton
```
 - closeButton
```
JButton closeButton
```
 - exportButton
```
JButton exportButton
```
 - fullInfoCheckBox
```
JCheckBox fullInfoCheckBox
```
 - fuzzyCheckBox
```
JCheckBox fuzzyCheckBox
```
 - closeCheckBox
```
JCheckBox closeCheckBox
```
 - actions
```
List<E> actions
```
- Class fiji.util.gui.GenericDialogPlus extends GenericDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - windowIDs
```
int[] windowIDs
```
 - windowTitles
```
String[] windowTitles
```
- Class fiji.util.gui.JFrameCommandFinder extends CommandFinderBase implements Serializable
 - Serialized Fields
 - menuBar
```
JMenuBar menuBar
```
- Class fiji.util.gui.JImagePanel extends JComponent implements Serializable
 - Serialized Fields
 - imp
```
ij.ImagePlus imp
```
 - imageUpdated
```
boolean imageUpdated
```
 - srcRect
```
Rectangle srcRect
```
 - imageWidth
```
int imageWidth
```
 - imageHeight
```
int imageHeight
```
 - listStroke
```
BasicStroke listStroke
```
 - ij
```
ij.ImageJ ij
```
 - magnification
```
double magnification
```
 - dstWidth
```
int dstWidth
```
 - dstHeight
```
int dstHeight
```
 - xMouseStart
```
int xMouseStart
```
 - yMouseStart
```
int yMouseStart
```
 - xSrcStart
```
int xSrcStart
```
 - ySrcStart
```
int ySrcStart
```
 - flags
```
int flags
```
 - offScreenImage
```
Image offScreenImage
```
 - offScreenWidth
```
int offScreenWidth
```
 - offScreenHeight
```
int offScreenHeight
```
- Class fiji.util.gui.OverlayedImageCanvas extends ImageCanvas implements Serializable
 
 serialVersionUID:
 
 -9005735333215207618L
 - Serialized Fields
 - overlays
```
Collection<E> overlays
```
 - backBufferWidth
```
int backBufferWidth
```
 - backBufferHeight
```
int backBufferHeight
```
 - backBufferGraphics
```
Graphics backBufferGraphics
```
 - backBufferImage
```
Image backBufferImage
```
 - backBufferComposite
```
Composite backBufferComposite
```
Package hr.irb.fastRandomForest
- Class hr.irb.fastRandomForest.FastRandomForest extends AbstractClassifier implements Serializable
  
  serialVersionUID:
  
  4216839470751428700L
  - Serialized Fields
    - m_numTrees
```
int m_numTrees
```
      Number of trees in forest.
    - m_numFeatures
```
int m_numFeatures
```
      Number of features to consider in random feature selection. If less than 1 will use int(logM+1) )
    - m_randomSeed
```
int m_randomSeed
```
      The random seed.
    - m_KValue
```
int m_KValue
```
      Final number of features that were considered in last build.
    - m_NumThreads
```
int m_NumThreads
```
      Number of simultaneous threads to use in computation (0 = autodetect).
    - m_bagger
```
hr.irb.fastRandomForest.FastRfBagging m_bagger
```
      The bagger.
    - m_MaxDepth
```
int m_MaxDepth
```
      The maximum depth of the trees (0 = unlimited)
    - m_Info
```
Instances m_Info
```
      The header information.
    - m_ZeroR
```
AbstractClassifier m_ZeroR
```
      a ZeroR model in case no model can be built from the data
    - m_FeatureImportances
```
double[] m_FeatureImportances
```
      The value of the features importances.
    - m_computeImportances
```
boolean m_computeImportances
```
      Whether to compute the importances or not.
- Class hr.irb.fastRandomForest.FRFAttributeEval extends ASEvaluation implements Serializable
  
  serialVersionUID:
  
  -4504270948574160991L
  - Serialized Fields
    - m_Importances
```
double[] m_Importances
```
      The feature importances.
    - m_frfProto
```
FastRandomForest m_frfProto
```
      The prototype for the rf.

Package ij.gui

Class ij.gui.Arrow extends Line implements Serializable
- Serialized Fields
  - style
```
int style
```
  - headSize
```
double headSize
```
  - doubleHeaded
```
boolean doubleHeaded
```
  - outline
```
boolean outline
```
  - points
```
float[] points
```
  - path
```
GeneralPath path
```
  - headShaftRatio
```
double headShaftRatio
```
Class ij.gui.EllipseRoi extends PolygonRoi implements Serializable
- Serialized Fields
  - xstart
```
double xstart
```
  - ystart
```
double ystart
```
  - aspectRatio
```
double aspectRatio
```
  - handle
```
int[] handle
```
Class ij.gui.FreehandRoi extends PolygonRoi implements Serializable

Class ij.gui.GenericDialog extends Dialog implements Serializable

Serialized Fields

numberField
```
Vector<E> numberField
```
stringField
```
Vector<E> stringField
```
checkbox
```
Vector<E> checkbox
```
choice
```
Vector<E> choice
```
slider
```
Vector<E> slider
```
radioButtonGroups
```
Vector<E> radioButtonGroups
```
textArea1
```
TextArea textArea1
```
textArea2
```
TextArea textArea2
```
defaultValues
```
Vector<E> defaultValues
```
defaultText
```
Vector<E> defaultText
```
defaultStrings
```
Vector<E> defaultStrings
```
defaultChoiceIndexes
```
Vector<E> defaultChoiceIndexes
```
theLabel
```
Component theLabel
```
okay
```
Button okay
```
cancel
```
Button cancel
```
no
```
Button no
```
help
```
Button help
```
helpLabel
```
String helpLabel
```
wasCanceled
```
boolean wasCanceled
```
wasOKed
```
boolean wasOKed
```
nfIndex
```
int nfIndex
```
sfIndex
```
int sfIndex
```
cbIndex
```
int cbIndex
```
choiceIndex
```
int choiceIndex
```
textAreaIndex
```
int textAreaIndex
```
radioButtonIndex
```
int radioButtonIndex
```
c
```
GridBagConstraints c
```
firstNumericField
```
boolean firstNumericField
```
firstSlider
```
boolean firstSlider
```
invalidNumber
```
boolean invalidNumber
```
errorMessage
```
String errorMessage
```
labels
```
Hashtable<K,V> labels
```
macro
```
boolean macro
```
macroOptions
```
String macroOptions
```
addToSameRow
```
boolean addToSameRow
```
addToSameRowCalled
```
boolean addToSameRowCalled
```
topInset
```
int topInset
```
leftInset
```
int leftInset
```
bottomInset
```
int bottomInset
```
customInsets
```
boolean customInsets
```
sliderIndexes
```
Vector<E> sliderIndexes
```
sliderScales
```
Vector<E> sliderScales
```
sliderDigits
```
Vector<E> sliderDigits
```
previewCheckbox
```
Checkbox previewCheckbox
```
dialogListeners
```
Vector<E> dialogListeners
```
pfr
```
ij.plugin.filter.PlugInFilterRunner pfr
```
previewLabel
```
String previewLabel
```
recorderOn
```
boolean recorderOn
```
echoChar
```
char echoChar
```
hideCancelButton
```
boolean hideCancelButton
```
centerDialog
```
boolean centerDialog
```
helpURL
```
String helpURL
```
smartRecording
```
boolean smartRecording
```
imagePanels
```
Vector<E> imagePanels
```
firstPaint
```
boolean firstPaint
```
fontSizeSet
```
boolean fontSizeSet
```
showDialogCalled
```
boolean showDialogCalled
```
optionsRecorded
```
boolean optionsRecorded
```
lastLabelAdded
```
Label lastLabelAdded
```
windowIDs
```
int[] windowIDs
```
windowTitles
```
String[] windowTitles
```

Class ij.gui.HistogramWindow extends ImageWindow implements Serializable

Serialized Fields

stats
```
ij.process.ImageStatistics stats
```
histogram
```
long[] histogram
```
lut
```
ij.LookUpTable lut
```
frame
```
Rectangle frame
```
list
```
Button list
```
save
```
Button save
```
copy
```
Button copy
```
log
```
Button log
```
live
```
Button live
```
rgb
```
Button rgb
```
value
```
Label value
```
count
```
Label count
```
decimalPlaces
```
int decimalPlaces
```
digits
```
int digits
```
newMaxCount
```
long newMaxCount
```
plotScale
```
int plotScale
```
logScale
```
boolean logScale
```
cal
```
ij.measure.Calibration cal
```
yMax
```
int yMax
```
srcImageID
```
int srcImageID
```
srcImp
```
ij.ImagePlus srcImp
```
bgThread
```
Thread bgThread
```
doUpdate
```
boolean doUpdate
```
rgbMode
```
int rgbMode
```
blankLabel
```
String blankLabel
```
stackHistogram
```
boolean stackHistogram
```
font
```
Font font
```
showBins
```
boolean showBins
```
col1
```
int col1
```
col2
```
int col2
```
row1
```
int row1
```
row2
```
int row2
```
row3
```
int row3
```
row4
```
int row4
```
row5
```
int row5
```

Class ij.gui.HTMLDialog extends JDialog implements Serializable
- Serialized Fields
  - escapePressed
```
boolean escapePressed
```
  - editorPane
```
JEditorPane editorPane
```
  - modal
```
boolean modal
```

Class ij.gui.ImageCanvas extends Canvas implements Serializable

Serialized Fields

imp
```
ij.ImagePlus imp
```
imageUpdated
```
boolean imageUpdated
```
srcRect
```
Rectangle srcRect
```
imageWidth
```
int imageWidth
```
imageHeight
```
int imageHeight
```
xMouse
```
int xMouse
```
yMouse
```
int yMouse
```
showCursorStatus
```
boolean showCursorStatus
```
sx2
```
int sx2
```
sy2
```
int sy2
```
disablePopupMenu
```
boolean disablePopupMenu
```
font
```
Font font
```
labelRects
```
Rectangle[] labelRects
```
maxBoundsReset
```
boolean maxBoundsReset
```
showAllOverlay
```
Overlay showAllOverlay
```
defaultColor
```
Color defaultColor
```
resetMaxBoundsCount
```
int resetMaxBoundsCount
```
currentRoi
```
Roi currentRoi
```
mousePressedX
```
int mousePressedX
```
mousePressedY
```
int mousePressedY
```
mousePressedTime
```
long mousePressedTime
```
overOverlayLabel
```
boolean overOverlayLabel
```
lastZoomSX
```
int lastZoomSX
```
lastZoomSY
```
int lastZoomSY
```
zoomTargetOX
```
int zoomTargetOX
```
zoomTargetOY
```
int zoomTargetOY
```
ij
```
ij.ImageJ ij
```
magnification
```
double magnification
```
dstWidth
```
int dstWidth
```
dstHeight
```
int dstHeight
```
xMouseStart
```
int xMouseStart
```
yMouseStart
```
int yMouseStart
```
xSrcStart
```
int xSrcStart
```
ySrcStart
```
int ySrcStart
```
flags
```
int flags
```
offScreenImage
```
Image offScreenImage
```
offScreenWidth
```
int offScreenWidth
```
offScreenHeight
```
int offScreenHeight
```
mouseExited
```
boolean mouseExited
```
customRoi
```
boolean customRoi
```
drawNames
```
boolean drawNames
```
paintPending
```
AtomicBoolean paintPending
```
scaleToFit
```
boolean scaleToFit
```
painted
```
boolean painted
```
hideZoomIndicator
```
boolean hideZoomIndicator
```
flattening
```
boolean flattening
```
pressTimer
```
Timer pressTimer
```
roiPopupMenu
```
PopupMenu roiPopupMenu
```
firstFrame
```
long firstFrame
```
frames
```
int frames
```
fps
```
int fps
```

Class ij.gui.ImagePanel extends Panel implements Serializable
- Serialized Fields
  - img
```
ij.ImagePlus img
```
  - width
```
int width
```
  - height
```
int height
```
Class ij.gui.ImageRoi extends Roi implements Serializable
- Serialized Fields
  - img
```
Image img
```
  - composite
```
Composite composite
```
  - opacity
```
double opacity
```
  - angle
```
double angle
```
  - zeroTransparent
```
boolean zeroTransparent
```
  - ip
```
ij.process.ImageProcessor ip
```

Class ij.gui.ImageWindow extends Frame implements Serializable

Serialized Fields

imp
```
ij.ImagePlus imp
```
ij
```
ij.ImageJ ij
```
ic
```
ImageCanvas ic
```
initialMagnification
```
double initialMagnification
```
newWidth
```
int newWidth
```
newHeight
```
int newHeight
```
closed
```
boolean closed
```
newCanvas
```
boolean newCanvas
```
unzoomWhenMinimizing
```
boolean unzoomWhenMinimizing
```
maxWindowBounds
```
Rectangle maxWindowBounds
```
maxBounds
```
Rectangle maxBounds
```
setMaxBoundsTime
```
long setMaxBoundsTime
```
sliderHeight
```
int sliderHeight
```
SCALE
```
double SCALE
```
TEXT_GAP
```
int TEXT_GAP
```
textGap
```
int textGap
```
initialLoc
```
Point initialLoc
```
screenHeight
```
int screenHeight
```
screenWidth
```
int screenWidth
```
running
```
boolean running
```
running2
```
boolean running2
```

Class ij.gui.Line extends Roi implements Serializable

Serialized Fields

x1
```
int x1
```
y1
```
int y1
```
x2
```
int x2
```
y2
```
int y2
```
x1d
```
double x1d
```
y1d
```
double y1d
```
x2d
```
double x2d
```
y2d
```
double y2d
```
x1R
```
double x1R
```
y1R
```
double y1R
```
x2R
```
double x2R
```
y2R
```
double y2R
```
startxd
```
double startxd
```
startyd
```
double startyd
```
dragged
```
boolean dragged
```
mouseUpCount
```
int mouseUpCount
```

Class ij.gui.MessageDialog extends Dialog implements Serializable
- Serialized Fields
  - button
```
Button button
```
  - label
```
MultiLineLabel label
```
  - escapePressed
```
boolean escapePressed
```
Class ij.gui.MultiLineLabel extends Canvas implements Serializable
- Serialized Fields
  - lines
```
String[] lines
```
  - num_lines
```
int num_lines
```
  - margin_width
```
int margin_width
```
  - margin_height
```
int margin_height
```
  - line_height
```
int line_height
```
  - line_ascent
```
int line_ascent
```
  - line_widths
```
int[] line_widths
```
  - min_width
```
int min_width
```
  - max_width
```
int max_width
```
Class ij.gui.NonBlockingGenericDialog extends GenericDialog implements Serializable
- Serialized Fields
  - imp
```
ij.ImagePlus imp
```
  - windowListener
```
WindowListener windowListener
```
Class ij.gui.OvalRoi extends Roi implements Serializable
Class ij.gui.PlotCanvas extends ImageCanvas implements Serializable
- Serialized Fields
  - plot
```
Plot plot
```
  - xScrolled
```
int xScrolled
```
  - yScrolled
```
int yScrolled
```
  - oldWidth
```
int oldWidth
```
  - oldHeight
```
int oldHeight
```
  - rangeArrowIndexWhenPressed
```
int rangeArrowIndexWhenPressed
```

Class ij.gui.PlotWindow extends ImageWindow implements Serializable

Serialized Fields

wasActivated
```
boolean wasActivated
```
list
```
Button list
```
data
```
Button data
```
more
```
Button more
```
live
```
Button live
```
dataPopupMenu
```
PopupMenu dataPopupMenu
```
morePopupMenu
```
PopupMenu morePopupMenu
```
menuItems
```
MenuItem[] menuItems
```
statusLabel
```
Label statusLabel
```
userStatusText
```
String userStatusText
```
defaultDigits
```
int defaultDigits
```
markSize
```
int markSize
```
plot
```
Plot plot
```
plotMaker
```
PlotMaker plotMaker
```
srcImp
```
ij.ImagePlus srcImp
```
bgThread
```
Thread bgThread
```
doUpdate
```
boolean doUpdate
```
rangeArrowRois
```
Roi[] rangeArrowRois
```
rangeArrowsVisible
```
boolean rangeArrowsVisible
```
activeRangeArrow
```
int activeRangeArrow
```

Class ij.gui.PointRoi extends PolygonRoi implements Serializable

Serialized Fields

showLabels
```
boolean showLabels
```
type
```
int type
```
size
```
int size
```
counter
```
int counter
```
nCounters
```
int nCounters
```
counters
```
short[] counters
```
positions
```
int[] positions
```
counts
```
int[] counts
```
rt
```
ij.measure.ResultsTable rt
```
lastPointTime
```
long lastPointTime
```
counterInfo
```
int[] counterInfo
```
promptBeforeDeleting
```
boolean promptBeforeDeleting
```
promptBeforeDeletingCalled
```
boolean promptBeforeDeletingCalled
```
nMarkers
```
int nMarkers
```
addToOverlay
```
boolean addToOverlay
```

Class ij.gui.PolygonRoi extends Roi implements Serializable

Serialized Fields

maxPoints
```
int maxPoints
```
xp
```
int[] xp
```
yp
```
int[] yp
```
xpf
```
float[] xpf
```
ypf
```
float[] ypf
```
xp2
```
int[] xp2
```
yp2
```
int[] yp2
```
nPoints
```
int nPoints
```
xSpline
```
float[] xSpline
```
ySpline
```
float[] ySpline
```
splinePoints
```
int splinePoints
```
clip
```
Rectangle clip
```
angle1
```
double angle1
```
degrees
```
double degrees
```
xClipMin
```
int xClipMin
```
yClipMin
```
int yClipMin
```
xClipMax
```
int xClipMax
```
yClipMax
```
int yClipMax
```
userCreated
```
boolean userCreated
```
boxSize
```
int boxSize
```
mouseUpTime
```
long mouseUpTime
```

Class ij.gui.ProgressBar extends Canvas implements Serializable

Serialized Fields

canvasWidth
```
int canvasWidth
```
canvasHeight
```
int canvasHeight
```
x
```
int x
```
y
```
int y
```
width
```
int width
```
height
```
int height
```
lastTime
```
long lastTime
```
showBar
```
boolean showBar
```
batchMode
```
boolean batchMode
```
barColor
```
Color barColor
```
fillColor
```
Color fillColor
```
backgroundColor
```
Color backgroundColor
```
frameBrighter
```
Color frameBrighter
```
frameDarker
```
Color frameDarker
```
dualDisplay
```
boolean dualDisplay
```
slowX
```
double slowX
```
fastX
```
double fastX
```

Class ij.gui.Roi extends Object implements Serializable

Serialized Fields

startX
```
int startX
```
startY
```
int startY
```
x
```
int x
```
y
```
int y
```
width
```
int width
```
height
```
int height
```
startXD
```
double startXD
```
startYD
```
double startYD
```
bounds
```
Rectangle2D.Double bounds
```
activeHandle
```
int activeHandle
```
state
```
int state
```
modState
```
int modState
```
cornerDiameter
```
int cornerDiameter
```
previousSX
```
int previousSX
```
previousSY
```
int previousSY
```
type
```
int type
```
xMax
```
int xMax
```
yMax
```
int yMax
```
imp
```
ij.ImagePlus imp
```
imageID
```
int imageID
```
ic
```
ImageCanvas ic
```
oldX
```
int oldX
```
oldY
```
int oldY
```
oldWidth
```
int oldWidth
```
oldHeight
```
int oldHeight
```
clipX
```
int clipX
```
clipY
```
int clipY
```
clipWidth
```
int clipWidth
```
clipHeight
```
int clipHeight
```
clipboard
```
ij.ImagePlus clipboard
```
constrain
```
boolean constrain
```
center
```
boolean center
```
aspect
```
boolean aspect
```
updateFullWindow
```
boolean updateFullWindow
```
mag
```
double mag
```
asp_bk
```
double asp_bk
```
cachedMask
```
ij.process.ImageProcessor cachedMask
```
handleColor
```
Color handleColor
```
strokeColor
```
Color strokeColor
```
instanceColor
```
Color instanceColor
```
fillColor
```
Color fillColor
```
stroke
```
BasicStroke stroke
```
nonScalable
```
boolean nonScalable
```
overlay
```
boolean overlay
```
wideLine
```
boolean wideLine
```
ignoreClipRect
```
boolean ignoreClipRect
```
flattenScale
```
double flattenScale
```
name
```
String name
```
position
```
int position
```
channel
```
int channel
```
slice
```
int slice
```
frame
```
int frame
```
hyperstackPosition
```
boolean hyperstackPosition
```
prototypeOverlay
```
Overlay prototypeOverlay
```
subPixel
```
boolean subPixel
```
activeOverlayRoi
```
boolean activeOverlayRoi
```
props
```
Properties props
```
isCursor
```
boolean isCursor
```
xcenter
```
double xcenter
```
ycenter
```
double ycenter
```
listenersNotified
```
boolean listenersNotified
```
antiAlias
```
boolean antiAlias
```
group
```
int group
```
usingDefaultStroke
```
boolean usingDefaultStroke
```
handleSize
```
int handleSize
```
scaleStrokeWidth
```
boolean scaleStrokeWidth
```

Class ij.gui.RotatedRectRoi extends PolygonRoi implements Serializable
- Serialized Fields
  - xstart
```
double xstart
```
  - ystart
```
double ystart
```
  - rectWidth
```
double rectWidth
```
Class ij.gui.SaveChangesDialog extends Dialog implements Serializable
- Serialized Fields
  - dontSave
```
Button dontSave
```
  - cancel
```
Button cancel
```
  - save
```
Button save
```
  - cancelPressed
```
boolean cancelPressed
```
  - savePressed
```
boolean savePressed
```
Class ij.gui.ScrollbarWithLabel extends Panel implements Serializable
- Serialized Fields
  - bar
```
Scrollbar bar
```
  - icon
```
ij.gui.ScrollbarWithLabel.Icon icon
```
  - stackWindow
```
StackWindow stackWindow
```
Class ij.gui.ShapeRoi extends Roi implements Serializable
- Serialized Fields
 - shape
```
Shape shape
```
 - maxerror
```
double maxerror
```
 - flatness
```
double flatness
```
 - maxPoly
```
int maxPoly
```
 - flatten
```
boolean flatten
```
 - forceTrace
```
boolean forceTrace
```
 - forceAngle
```
boolean forceAngle
```
 - savedRois
```
Vector<E> savedRois
```
Class ij.gui.ShapeRoiHelper extends ShapeRoi implements Serializable

serialVersionUID:

3683518238872064558L

Class ij.gui.StackWindow extends ImageWindow implements Serializable

Serialized Fields

sliceSelector
```
Scrollbar sliceSelector
```
cSelector
```
ScrollbarWithLabel cSelector
```
zSelector
```
ScrollbarWithLabel zSelector
```
tSelector
```
ScrollbarWithLabel tSelector
```
thread
```
Thread thread
```
done
```
boolean done
```
slice
```
int slice
```
animationSelector
```
ScrollbarWithLabel animationSelector
```
hyperStack
```
boolean hyperStack
```
nChannels
```
int nChannels
```
nSlices
```
int nSlices
```
nFrames
```
int nFrames
```
c
```
int c
```
z
```
int z
```
t
```
int t
```

Class ij.gui.TextRoi extends Roi implements Serializable
- Serialized Fields
  - theText
```
String[] theText
```
  - font
```
Font font
```
  - justification
```
int justification
```
  - previousMag
```
double previousMag
```
  - firstChar
```
boolean firstChar
```
  - firstMouseUp
```
boolean firstMouseUp
```
  - angle
```
double angle
```
  - previousRoi
```
Roi previousRoi
```
  - fontGraphics
```
Graphics fontGraphics
```

Class ij.gui.Toolbar extends Canvas implements Serializable

Serialized Fields

ps
```
Dimension ps
```
down
```
boolean[] down
```
previousTool
```
int previousTool
```
x
```
int x
```
y
```
int y
```
xOffset
```
int xOffset
```
yOffset
```
int yOffset
```
mouseDownTime
```
long mouseDownTime
```
g
```
Graphics g
```
mpPrevious
```
int mpPrevious
```
names
```
String[] names
```
icons
```
String[] icons
```
tools
```
ij.plugin.tool.PlugInTool[] tools
```
menus
```
PopupMenu[] menus
```
nExtraTools
```
int nExtraTools
```
macroInstaller
```
ij.plugin.MacroInstaller macroInstaller
```
addingSingleTool
```
boolean addingSingleTool
```
installingStartupTool
```
boolean installingStartupTool
```
doNotSavePrefs
```
boolean doNotSavePrefs
```
pc
```
int pc
```
icon
```
String icon
```
startupTime
```
int startupTime
```
rectPopup
```
PopupMenu rectPopup
```
ovalPopup
```
PopupMenu ovalPopup
```
pointPopup
```
PopupMenu pointPopup
```
linePopup
```
PopupMenu linePopup
```
zoomPopup
```
PopupMenu zoomPopup
```
pickerPopup
```
PopupMenu pickerPopup
```
switchPopup
```
PopupMenu switchPopup
```
rectItem
```
CheckboxMenuItem rectItem
```
roundRectItem
```
CheckboxMenuItem roundRectItem
```
rotatedRectItem
```
CheckboxMenuItem rotatedRectItem
```
ovalItem
```
CheckboxMenuItem ovalItem
```
ellipseItem
```
CheckboxMenuItem ellipseItem
```
brushItem
```
CheckboxMenuItem brushItem
```
pointItem
```
CheckboxMenuItem pointItem
```
multiPointItem
```
CheckboxMenuItem multiPointItem
```
straightLineItem
```
CheckboxMenuItem straightLineItem
```
polyLineItem
```
CheckboxMenuItem polyLineItem
```
freeLineItem
```
CheckboxMenuItem freeLineItem
```
arrowItem
```
CheckboxMenuItem arrowItem
```
currentSet
```
String currentSet
```
pressTimer
```
Timer pressTimer
```
lineType
```
int lineType
```
gray
```
Color gray
```
brighter
```
Color brighter
```
darker
```
Color darker
```
evenDarker
```
Color evenDarker
```
triangleColor
```
Color triangleColor
```
toolColor
```
Color toolColor
```

Class ij.gui.TrimmedButton extends Button implements Serializable
- Serialized Fields
  - trim
```
int trim
```
Class ij.gui.WaitForUserDialog extends Dialog implements Serializable
- Serialized Fields
  - button
```
Button button
```
  - label
```
MultiLineLabel label
```
  - escPressed
```
boolean escPressed
```
Class ij.gui.YesNoCancelDialog extends Dialog implements Serializable
- Serialized Fields
  - yesB
```
Button yesB
```
  - noB
```
Button noB
```
  - cancelB
```
Button cancelB
```
  - cancelPressed
```
boolean cancelPressed
```
  - yesPressed
```
boolean yesPressed
```
  - firstPaint
```
boolean firstPaint
```

Package ij3d

Class ij3d.Image3DMenubar extends JMenuBar implements Serializable

Serialized Fields

univ
```
Image3DUniverse univ
```
executer
```
Executer executer
```
open
```
JMenuItem open
```
addContentFromImage
```
JMenuItem addContentFromImage
```
saveView
```
JMenuItem saveView
```
loadView
```
JMenuItem loadView
```
saveSession
```
JMenuItem saveSession
```
loadSession
```
JMenuItem loadSession
```
importObj
```
JMenuItem importObj
```
importStl
```
JMenuItem importStl
```
color
```
JMenuItem color
```
bgColor
```
JMenuItem bgColor
```
fullscreen
```
JCheckBoxMenuItem fullscreen
```
channels
```
JMenuItem channels
```
luts
```
JMenuItem luts
```
transparency
```
JMenuItem transparency
```
threshold
```
JMenuItem threshold
```
delete
```
JMenuItem delete
```
properties
```
JMenuItem properties
```
resetView
```
JMenuItem resetView
```
snapshot
```
JMenuItem snapshot
```
record360
```
JMenuItem record360
```
startRecord
```
JMenuItem startRecord
```
stopRecord
```
JMenuItem stopRecord
```
startAnimation
```
JMenuItem startAnimation
```
stopAnimation
```
JMenuItem stopAnimation
```
animationOptions
```
JMenuItem animationOptions
```
light
```
JMenuItem light
```
viewPreferences
```
JMenuItem viewPreferences
```
shortcuts
```
JMenuItem shortcuts
```
close
```
JMenuItem close
```
setTransform
```
JMenuItem setTransform
```
resetTransform
```
JMenuItem resetTransform
```
applyTransform
```
JMenuItem applyTransform
```
saveTransform
```
JMenuItem saveTransform
```
exportTransformed
```
JMenuItem exportTransformed
```
exportObj
```
JMenuItem exportObj
```
exportDXF
```
JMenuItem exportDXF
```
exportAsciiSTL
```
JMenuItem exportAsciiSTL
```
exportBinarySTL
```
JMenuItem exportBinarySTL
```
exportU3D
```
JMenuItem exportU3D
```
scalebar
```
JMenuItem scalebar
```
displayAsVolume
```
JMenuItem displayAsVolume
```
displayAsOrtho
```
JMenuItem displayAsOrtho
```
displayAsMultiOrtho
```
JMenuItem displayAsMultiOrtho
```
displayAsSurface
```
JMenuItem displayAsSurface
```
displayAsSurfacePlot
```
JMenuItem displayAsSurfacePlot
```
centerSelected
```
JMenuItem centerSelected
```
centerOrigin
```
JMenuItem centerOrigin
```
centerUniverse
```
JMenuItem centerUniverse
```
sync
```
JCheckBoxMenuItem sync
```
fitViewToUniverse
```
JMenuItem fitViewToUniverse
```
fitViewToContent
```
JMenuItem fitViewToContent
```
regist
```
JMenuItem regist
```
pl_load
```
JMenuItem pl_load
```
pl_save
```
JMenuItem pl_save
```
pl_size
```
JMenuItem pl_size
```
pl_color
```
JMenuItem pl_color
```
pl_show
```
JCheckBoxMenuItem pl_show
```
j3dproperties
```
JMenuItem j3dproperties
```
coordinateSystem
```
JCheckBoxMenuItem coordinateSystem
```
boundingBox
```
JCheckBoxMenuItem boundingBox
```
allCoordinateSystems
```
JCheckBoxMenuItem allCoordinateSystems
```
lock
```
JCheckBoxMenuItem lock
```
show
```
JCheckBoxMenuItem show
```
viewposXY
```
JMenuItem viewposXY
```
viewposXZ
```
JMenuItem viewposXZ
```
viewposYZ
```
JMenuItem viewposYZ
```
viewnegXY
```
JMenuItem viewnegXY
```
viewnegXZ
```
JMenuItem viewnegXZ
```
viewnegYZ
```
JMenuItem viewnegYZ
```
sphere
```
JMenuItem sphere
```
box
```
JMenuItem box
```
cone
```
JMenuItem cone
```
tube
```
JMenuItem tube
```
transformMenu
```
JMenu transformMenu
```
landmarksMenu
```
JMenu landmarksMenu
```
editMenu
```
JMenu editMenu
```
selectMenu
```
JMenu selectMenu
```
viewMenu
```
JMenu viewMenu
```
fileMenu
```
JMenu fileMenu
```
helpMenu
```
JMenu helpMenu
```
addMenu
```
JMenu addMenu
```

Class ij3d.ImageCanvas3D extends Canvas3D implements Serializable

Serialized Fields

roiImagePlus

ij3d.ImageCanvas3D.RoiImagePlus roiImagePlus

roiImageCanvas
```
ImageCanvas roiImageCanvas
```
pressed
```
Map<K,V> pressed
```
released
```
Map<K,V> released
```
background
```
Background background
```
ui
```
UIAdapter ui
```
exec
```
ExecutorService exec
```

Class ij3d.ImageWindow3D extends JFrame implements Serializable

Serialized Fields

universe
```
DefaultUniverse universe
```
canvas3D
```
ImageCanvas3D canvas3D
```
status
```
Label status
```
noOffScreen
```
boolean noOffScreen
```

error_listener

ij3d.ImageWindow3D.ErrorListener error_listener

imp
```
ij.ImagePlus imp
```
offScreenCanvas3D
```
Canvas3D offScreenCanvas3D
```

imp_updater

ij3d.ImageWindow3D.ImagePlusUpdater imp_updater

top
```
int top
```
bottom
```
int bottom
```
left
```
int left
```
right
```
int right
```
lastToolID
```
int lastToolID
```

Class ij3d.RegistrationMenubar extends JMenuBar implements Serializable
- Serialized Fields
 - univ
```
Image3DUniverse univ
```
 - register
```
JMenu register
```
 - exit
```
JMenuItem exit
```
 - adjustSlices
```
JMenuItem adjustSlices
```
 - openDialogs
```
List<E> openDialogs
```
 - templ
```
Content templ
```
 - model
```
Content model
```

Package ij3d.gui

Class ij3d.gui.InteractiveTransformDialog extends GenericDialog implements Serializable
- Serialized Fields
  - axis
```
Vector3f axis
```
  - origin
```
Vector3f origin
```
  - angle
```
float angle
```
  - translation
```
Vector3f translation
```
  - contentCenter
```
Point3f contentCenter
```
  - axisTF
```
TextField axisTF
```
  - angleTF
```
TextField angleTF
```
  - originTF
```
TextField originTF
```
  - translationTF
```
TextField translationTF
```
  - matrixTA
```
TextArea matrixTA
```

Class ij3d.gui.LUTDialog extends GenericDialog implements Serializable

Serialized Fields

listeners
```
ArrayList<E> listeners
```
repainter
```
ij3d.gui.LUTDialog.Repainter repainter
```
tool
```
ij3d.gui.LUTDialog.ChannelsTool tool
```
rOld
```
int[] rOld
```
gOld
```
int[] gOld
```
bOld
```
int[] bOld
```
aOld
```
int[] aOld
```
r
```
int[] r
```
g
```
int[] g
```
b
```
int[] b
```
a
```
int[] a
```

Package ij3d.pointlist
- Class ij3d.pointlist.PointListDialog extends Dialog implements Serializable
  - Serialized Fields
    - c
```
GridBagConstraints c
```
      The constraints for the layout.
    - gridbag
```
GridBagLayout gridbag
```
      The layout itself
    - panel
```
Panel panel
```
      The parent panel of the PointListPanels
    - extraPanel
```
Panel extraPanel
```
      An additional panel which is layed out at the bottom of the window and may be used for showing some buttons.
- Class ij3d.pointlist.PointListPanel extends Panel implements Serializable
  - Serialized Fields
    - points
```
PointList points
```
      A reference to the actual PointList
    - c
```
GridBagConstraints c
```
      The constraints used by the layout
    - popup
```
PopupMenu popup
```
      The popup menu
    - current
```
BenesNamedPoint current
```
      The point under the cursor when opening the popup menu
    - df
```
DecimalFormat df
```
      The format for pretty printing points
    - header
```
String header
```
      The header of the list
    - grey
```
Color grey
```
Package ij3d.shortcuts
- Class ij3d.shortcuts.ShortCutDialog extends JDialog implements Serializable
- Class ij3d.shortcuts.ShortCutTable extends JTable implements Serializable
Package ini.trakem2.display
- Class ini.trakem2.display.Channel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - c
```
JCheckBox c
```
 - display
```
Display display
```
 - channel
```
int channel
```
 - alpha
```
float alpha
```
- Class ini.trakem2.display.DisplayablePanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - c
```
JCheckBox c
```
 - c_locked
```
JCheckBox c_locked
```
 - c_linked
```
JCheckBox c_linked
```
 - title
```
JLabel title
```
 - title2
```
JLabel title2
```
 - idlabel
```
JLabel idlabel
```
 - titles
```
JPanel titles
```
 - sp
```
SnapshotPanel sp
```
 - display
```
Display display
```
 - d
```
Displayable d
```
 - listener
```
ini.trakem2.display.DisplayablePanel.ML listener
```
- Class ini.trakem2.display.DisplayCanvas extends ImageCanvas implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - display
```
Display display
```
 - update_graphics
```
boolean update_graphics
```
 - offscreen
```
BufferedImage offscreen
```
 - to_flush
```
HashSet<E> to_flush
```
 - al_top
```
ArrayList<E> al_top
```
 - lock_paint
```
Lock lock_paint
```
 - box
```
Rectangle box
```
 - fake_win
```
FakeImageWindow fake_win
```
 - freehandProfile
```
FreeHandProfile freehandProfile
```
 - r
```
Robot r
```
 - offscreen_lock
```
Object offscreen_lock
```
 - noCursor
```
Cursor noCursor
```
 - snapping
```
boolean snapping
```
 - dragging
```
boolean dragging
```
 - input_disabled
```
boolean input_disabled
```
 - input_disabled2
```
boolean input_disabled2
```
 - volatileImage
```
VolatileImage volatileImage
```
 - volatile_lock
```
Object volatile_lock
```
 - invalid_volatile
```
boolean invalid_volatile
```
 - RT
```
AbstractRepaintThread RT
```
 Handles repaint event requests and the generation of offscreen threads.
 - stroke
```
BasicStroke stroke
```
 Paint lines always with a thickness of 1 pixel. This stroke is modified when the magnification is changed, to compensate.
 - atc
```
AffineTransform atc
```
 The affine transform representing the srcRect displacement and the magnification.
 - x_p
```
int x_p
```
 As offscreen.
 - y_p
```
int y_p
```
 As offscreen.
 - x_d
```
int x_d
```
 As offscreen.
 - y_d
```
int y_d
```
 As offscreen.
 - x_d_old
```
int x_d_old
```
 As offscreen.
 - y_d_old
```
int y_d_old
```
 As offscreen.
 - popup
```
boolean popup
```
 - locked
```
boolean locked
```
 - tmp_tool
```
int tmp_tool
```
 - last_popup
```
Point last_popup
```
 In world coordinates.
 - mouse_in
```
boolean mouse_in
```
 - old_brush_box
```
Rectangle old_brush_box
```
 - mouse_moved
```
ini.trakem2.display.DisplayCanvas.MouseMovedThread mouse_moved
```
 - last_keyCode
```
int last_keyCode
```
 - tagging
```
boolean tagging
```
 - animator
```
ScheduledExecutorService animator
```
 - zoom_and_pan
```
boolean zoom_and_pan
```
 - sfs
```
Vector<E> sfs
```
- Class ini.trakem2.display.DisplayNavigator extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - display
```
Display display
```
 - layer
```
Layer layer
```
 - hs_painted
```
Set<E> hs_painted
```
 - image
```
BufferedImage image
```
 - redraw_displayables
```
boolean redraw_displayables
```
 - scale
```
double scale
```
 - srcRect
```
Rectangle srcRect
```
 - x_p
```
int x_p
```
 - y_p
```
int y_p
```
 - new_x_old
```
int new_x_old
```
 - new_y_old
```
int new_y_old
```
 - offscreen_lock
```
Object offscreen_lock
```
 - to_flush
```
HashSet<E> to_flush
```
 - volatileImage
```
VolatileImage volatileImage
```
 - volatile_lock
```
Object volatile_lock
```
 - invalid_volatile
```
boolean invalid_volatile
```
 - snapshots_mode
```
int snapshots_mode
```
 - RT
```
AbstractRepaintThread RT
```
 Handles repaint event requests and the generation of offscreen threads.
 - drag
```
boolean drag
```
- Class ini.trakem2.display.FakeImageWindow extends ImageWindow implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - display
```
Display display
```
- Class ini.trakem2.display.LayerPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - title
```
JLabel title
```
 - slider
```
JSlider slider
```
 - color
```
Color color
```
 - alpha
```
float alpha
```
 - display
```
Display display
```
 - layer
```
Layer layer
```
- Class ini.trakem2.display.RollingPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - display
```
Display display
```
 - clazz
```
Class<T> clazz
```
 - current
```
Map<K,V> current
```
 - inner
```
JPanel inner
```
 - filler
```
JPanel filler
```
 - scrollBar
```
JScrollBar scrollBar
```
 - gbInner
```
GridBagLayout gbInner
```
 - cInner
```
GridBagConstraints cInner
```
- Class ini.trakem2.display.SnapshotPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - display
```
Display display
```
 - d
```
Displayable d
```
 - img
```
BufferedImage img
```
- Class ini.trakem2.display.YesNoDialog extends Dialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - yesB
```
Button yesB
```
 - noB
```
Button noB
```
 - yesPressed
```
boolean yesPressed
```
 - firstPaint
```
boolean firstPaint
```
 - closing_task
```
Runnable closing_task
```
Package ini.trakem2.imaging
- Class ini.trakem2.imaging.ContrastPlot extends Canvas implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - defaultMin
```
double defaultMin
```
    - defaultMax
```
double defaultMax
```
    - min
```
double min
```
    - max
```
double max
```
    - histogram
```
int[] histogram
```
    - hmax
```
int hmax
```
    - os
```
Image os
```
    - color
```
Color color
```
Package ini.trakem2.tree
- Class ini.trakem2.tree.DNDTree extends JTree implements Serializable
  - Serialized Fields
    - autoscrollInsets
```
Insets autoscrollInsets
```
    - dtth
```
DefaultTreeTransferHandler dtth
```
    - dispatcher
```
Dispatcher dispatcher
```
    - project
```
Project project
```
    - background
```
Color background
```
- Class ini.trakem2.tree.DNDTree.NodeRenderer extends DefaultTreeCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
- Class ini.trakem2.tree.LayerTree extends DNDTree implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - selected_node
```
DefaultMutableTreeNode selected_node
```
- Class ini.trakem2.tree.LayerTree.LayerThingNodeRender extends DNDTree.NodeRenderer implements Serializable
  
  serialVersionUID:
  
  1L
- Class ini.trakem2.tree.ProjectTree extends DNDTree implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - selected_node
```
DefaultMutableTreeNode selected_node
```
- Class ini.trakem2.tree.ProjectTree.ProjectThingNodeRenderer extends DNDTree.NodeRenderer implements Serializable
  
  serialVersionUID:
  
  1L
- Class ini.trakem2.tree.TemplateTree extends DNDTree implements Serializable
  - Serialized Fields
    - selected_node
```
DefaultMutableTreeNode selected_node
```
    - root
```
TemplateThing root
```
Package ini.trakem2.utils
- Class ini.trakem2.utils.IntegerField extends JTextField implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - maxDigits
```
int maxDigits
```
- Class ini.trakem2.utils.OptionPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - bl
```
GridBagLayout bl
```
 - c
```
GridBagConstraints c
```
 - tl
```
ActionListener tl
```
 - kl
```
KeyListener kl
```
 - mwl
```
MouseWheelListener mwl
```
 - numeric_fields
```
List<E> numeric_fields
```
 - checkboxes
```
List<E> checkboxes
```
 - choices
```
List<E> choices
```
 - all
```
List<E> all
```
 - setters
```
HashMap<K,V> setters
```
 - rows
```
int rows
```
- Class ini.trakem2.utils.TypedHashMap extends HashMap<K,V> implements Serializable
 
 serialVersionUID:
 
 -7817318751687157665L
Package jitk.spline
- Class jitk.spline.ThinPlateR2LogRSplineKernelTransform extends Object implements Serializable
  
  serialVersionUID:
  
  -972934724062617822L
  - Serialized Fields
    - ndims
```
int ndims
```
    - dMatrix
```
org.ejml.data.DenseMatrix64F dMatrix
```
    - aMatrix
```
double[][] aMatrix
```
    - bVector
```
double[] bVector
```
    - stiffness
```
double stiffness
```
    - wMatrixComputeD
```
boolean wMatrixComputeD
```
    - computeAffine
```
boolean computeAffine
```
    - nLandmarks
```
int nLandmarks
```
    - sourceLandmarks
```
double[][] sourceLandmarks
```
    - weights
```
double[] weights
```
    - tmpDisplacement
```
double[] tmpDisplacement
```
Package landmarks
- Class landmarks.NamedPointSet.PointsFileException extends Exception implements Serializable
- Class landmarks.ProgressCanvas extends ImageCanvas implements Serializable
 - Serialized Fields
 - imagePlus
```
ij.ImagePlus imagePlus
```
 - fixed_x
```
int fixed_x
```
 - fixed_y
```
int fixed_y
```
 - fixed_z
```
int fixed_z
```
 - transformed_x
```
int transformed_x
```
 - transformed_y
```
int transformed_y
```
 - transformed_z
```
int transformed_z
```
 - drawFixed
```
boolean drawFixed
```
 - drawTransformed
```
boolean drawTransformed
```
- Class landmarks.ProgressWindow extends StackWindow implements Serializable
 - Serialized Fields
 - width
```
int width
```
 - height
```
int height
```
 - depth
```
int depth
```
 - scoreFormatter
```
DecimalFormat scoreFormatter
```
 - distanceFormatter
```
DecimalFormat distanceFormatter
```
 - plugin
```
NamePoints plugin
```
 - fineTuneThreads
```
ArrayList<E> fineTuneThreads
```
 - useThis
```
Button useThis
```
 - cancel
```
Button cancel
```
 - refineBestSoFar
```
Button refineBestSoFar
```
 - lowestScore
```
Label lowestScore
```
 - triedSoFar
```
Label triedSoFar
```
 - moveToRefinedPoint
```
Button moveToRefinedPoint
```
 - moveToOriginalPoint
```
Button moveToOriginalPoint
```
 - distanceMoved
```
Label distanceMoved
```
 - bestSoFar
```
RegistrationResult bestSoFar
```
 - useTheResult
```
boolean useTheResult
```
 - progressCanvas
```
ProgressCanvas progressCanvas
```
 - notShowingBest
```
boolean notShowingBest
```
 - timeLastProgressUpdate
```
long timeLastProgressUpdate
```
Package lenscorrection
- Class lenscorrection.NonLinearTransform extends NonLinearCoordinateTransform implements Serializable
 - Serialized Fields
 - transField
```
double[][][] transField
```
 - precalculated
```
boolean precalculated
```
- Class lenscorrection.PolynomialModel2D extends AbstractModel<PolynomialModel2D> implements Serializable
 - Serialized Fields
 - nlt
```
NonLinearTransform nlt
```
 - affine
```
AbstractAffineModel2D<M extends AbstractAffineModel2D<M>> affine
```
 - lambda
```
float lambda
```

Package loci.plugins.config

Class loci.plugins.config.ConfigWindow extends JFrame implements Serializable

Serialized Fields

formatsListModel
```
DefaultListModel<E> formatsListModel
```
formatsList
```
JList<E> formatsList
```
formatInfo
```
JPanel formatInfo
```
extensions
```
JTextField extensions
```
sliceLabel
```
JTextField sliceLabel
```
enabledBox
```
JCheckBox enabledBox
```
windowlessBox
```
JCheckBox windowlessBox
```
upgradeBox
```
JCheckBox upgradeBox
```
libsListModel
```
DefaultListModel<E> libsListModel
```
libsList
```
JList<E> libsList
```
type
```
JTextField type
```
status
```
JTextField status
```
version
```
JTextField version
```
path
```
JTextField path
```
url
```
JTextField url
```
license
```
JTextField license
```
notes
```
JTextArea notes
```
installButton
```
JButton installButton
```
setSliceLabelButton
```
JButton setSliceLabelButton
```
resetSliceLabelButton
```
JButton resetSliceLabelButton
```
log
```
PrintWriter log
```

Class loci.plugins.config.InstallWizard extends JFrame implements Serializable

Package loci.plugins.in
- Class loci.plugins.in.ImporterMetadata extends HashMap<String,Object> implements Serializable
Package loci.plugins.shortcut
- Class loci.plugins.shortcut.ShortcutPanel extends JPanel implements Serializable
- Class loci.plugins.shortcut.ShortcutTransferHandler extends TransferHandler implements Serializable
  - Serialized Fields
    - shortcutPanel
```
ShortcutPanel shortcutPanel
```
      Associated shortcut panel.
Package loci.plugins.util
- Class loci.plugins.util.BrowserOptionsWindow extends JFrame implements Serializable
- Class loci.plugins.util.DataBrowser extends StackWindow implements Serializable
  - Serialized Fields
    - fpsSpin
```
JSpinner fpsSpin
```
    - animate
```
Button animate
```
    - options
```
Button options
```
    - metadata
```
Button metadata
```
    - anim
```
boolean anim
```
    - allowShow
```
boolean allowShow
```
    - metaWindow
```
XMLWindow metaWindow
```
    - optionsWindow
```
BrowserOptionsWindow optionsWindow
```
    - xml
```
String xml
```
    - zScroll
```
Scrollbar zScroll
```
    - cScroll
```
Scrollbar cScroll
```
    - tScroll
```
Scrollbar tScroll
```
    - cSliders
```
Scrollbar[] cSliders
```
    - cLengths
```
int[] cLengths
```
    - cIndex
```
int[] cIndex
```
- Class loci.plugins.util.SearchableWindow extends ij.text.TextWindow implements Serializable
  - Serialized Fields
    - panel
```
ij.text.TextPanel panel
```
    - index
```
int index
```
Package mpicbg.imagefeatures
- Class mpicbg.imagefeatures.Feature extends Object implements Serializable
 
 serialVersionUID:
 
 551364650592173605L
 - Serialized Fields
 - scale
```
double scale
```
 - orientation
```
double orientation
```
 - location
```
double[] location
```
 - descriptor
```
float[] descriptor
```
- Class mpicbg.imagefeatures.FloatArray2DSIFT.Param extends Object implements Serializable
 - Serialized Fields
 - fdSize
```
int fdSize
```
 Feature descriptor size. How many samples per row and column
 - fdBins
```
int fdBins
```
 Feature descriptor orientation bins How many bins per local histogram
 - maxOctaveSize
```
int maxOctaveSize
```
 Size limits for scale octaves in px: minOctaveSize < octave < maxOctaveSize
 - minOctaveSize
```
int minOctaveSize
```
 - steps
```
int steps
```
 Steps per Scale Octave
 - initialSigma
```
float initialSigma
```
 Initial sigma of each Scale Octave
Package mpicbg.imglib.exception
- Class mpicbg.imglib.exception.ImgLibException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package mpicbg.models
- Class mpicbg.models.AbstractAffineModel1D extends AbstractModel<M extends AbstractAffineModel1D<M>> implements Serializable
 
 serialVersionUID:
 
 -986558573112906689L
- Class mpicbg.models.AbstractAffineModel2D extends AbstractModel<M extends AbstractAffineModel2D<M>> implements Serializable
 
 serialVersionUID:
 
 -4601554609754736334L
- Class mpicbg.models.AbstractAffineModel3D extends AbstractModel<M extends AbstractAffineModel3D<M>> implements Serializable
 
 serialVersionUID:
 
 -7611859904219650457L
- Class mpicbg.models.AbstractModel extends Object implements Serializable
 
 serialVersionUID:
 
 -4649306649450399752L
 - Serialized Fields
 - cost
```
double cost
```
 The cost depends on what kind of algorithm is running. It is always true that a smaller cost is better than large cost
- Class mpicbg.models.AbstractMovingLeastSquaresTransform extends Object implements Serializable
 
 serialVersionUID:
 
 7058285996477613433L
 - Serialized Fields
 - model
```
Model<M extends Model<M>> model
```
 - alpha
```
double alpha
```
- Class mpicbg.models.AffineModel1D extends AbstractAffineModel1D<AffineModel1D> implements Serializable
 
 serialVersionUID:
 
 -6691788501310913119L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - isInvertible
```
boolean isInvertible
```
- Class mpicbg.models.AffineModel2D extends AbstractAffineModel2D<AffineModel2D> implements Serializable
 
 serialVersionUID:
 
 2323673888015396528L
 - Serialized Fields
 - m00
```
double m00
```
 - m10
```
double m10
```
 - m01
```
double m01
```
 - m11
```
double m11
```
 - m02
```
double m02
```
 - m12
```
double m12
```
 - i00
```
double i00
```
 - i10
```
double i10
```
 - i01
```
double i01
```
 - i11
```
double i11
```
 - i02
```
double i02
```
 - i12
```
double i12
```
 - isInvertible
```
boolean isInvertible
```
- Class mpicbg.models.AffineModel3D extends AbstractAffineModel3D<AffineModel3D> implements Serializable
 
 serialVersionUID:
 
 4591403097787254013L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m03
```
double m03
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m13
```
double m13
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - m23
```
double m23
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - i02
```
double i02
```
 - i03
```
double i03
```
 - i10
```
double i10
```
 - i11
```
double i11
```
 - i12
```
double i12
```
 - i13
```
double i13
```
 - i20
```
double i20
```
 - i21
```
double i21
```
 - i22
```
double i22
```
 - i23
```
double i23
```
 - isInvertible
```
boolean isInvertible
```
- Class mpicbg.models.ConstantAffineModel1D extends InvertibleConstantModel<A extends Model<A> & Affine1D<A> & InvertibleBoundable,ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable>> implements Serializable
 
 serialVersionUID:
 
 -3540327692126579857L
- Class mpicbg.models.ConstantModel extends AbstractModel<M extends ConstantModel<A,M>> implements Serializable
 
 serialVersionUID:
 
 4028319936789363770L
 - Serialized Fields
 - model
```
Model<M extends Model<M>> model
```
- Class mpicbg.models.CoordinateTransformList extends Object implements Serializable
 
 serialVersionUID:
 
 -2481949109498295648L
 - Serialized Fields
 - transforms
```
List<E> transforms
```
- Class mpicbg.models.CoordinateTransformMap2D extends Object implements Serializable
 
 serialVersionUID:
 
 4762150526295594608L
 - Serialized Fields
 - map
```
float[][] map
```
 target coordinates addressed interleaved as map[ row ][ 2 * column ] = x map[ row ][ 2 * column + 1 ] = y
 - width
```
int width
```
 - height
```
int height
```
- Class mpicbg.models.CoordinateTransformMesh extends TransformMesh implements Serializable
 
 serialVersionUID:
 
 678862124003647263L
- Class mpicbg.models.ElasticMovingLeastSquaresMesh extends MovingLeastSquaresMesh<M extends AbstractModel<M>> implements Serializable
 
 serialVersionUID:
 
 4370634883524169318L
 - Serialized Fields
 - fixedTiles
```
HashSet<E> fixedTiles
```
 - alpha
```
double alpha
```
- Class mpicbg.models.HomographyModel2D extends AbstractModel<HomographyModel2D> implements Serializable
 
 serialVersionUID:
 
 -6363462467119993852L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - i02
```
double i02
```
 - i10
```
double i10
```
 - i11
```
double i11
```
 - i12
```
double i12
```
 - i20
```
double i20
```
 - i21
```
double i21
```
 - i22
```
double i22
```
- Class mpicbg.models.IdentityModel extends AbstractModel<IdentityModel> implements Serializable
 
 serialVersionUID:
 
 6465657594415965070L
- Class mpicbg.models.IllDefinedDataPointsException extends Exception implements Serializable
 
 serialVersionUID:
 
 -8384893194524443449L
- Class mpicbg.models.InterpolatedAffineModel1D extends InvertibleInterpolatedModel<A extends Model<A> & Affine1D<A>,B extends Model & Affine1D,InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model & Affine1D>> implements Serializable
 
 serialVersionUID:
 
 2662227348414849267L
 - Serialized Fields
 - affine
```
AffineModel1D affine
```
 - afs
```
double[] afs
```
 - bfs
```
double[] bfs
```
- Class mpicbg.models.InterpolatedAffineModel2D extends InvertibleInterpolatedModel<A extends Model<A> & Affine2D<A>,B extends Model & Affine2D,InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model & Affine2D>> implements Serializable
 
 serialVersionUID:
 
 -5646709386458263066L
 - Serialized Fields
 - affine
```
AffineModel2D affine
```
 - afs
```
double[] afs
```
 - bfs
```
double[] bfs
```
- Class mpicbg.models.InterpolatedAffineModel3D extends InvertibleInterpolatedModel<A extends Model<A> & Affine3D<A>,B extends Model & Affine3D,InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model & Affine3D>> implements Serializable
 
 serialVersionUID:
 
 -6834487125812773082L
 - Serialized Fields
 - affine
```
AffineModel3D affine
```
 - afs
```
double[] afs
```
 - bfs
```
double[] bfs
```
- Class mpicbg.models.InterpolatedCoordinateTransform extends Object implements Serializable
 
 serialVersionUID:
 
 8356592128041276188L
 - Serialized Fields
 - a
```
CoordinateTransform a
```
 - b
```
CoordinateTransform b
```
 - lambda
```
double lambda
```
- Class mpicbg.models.InterpolatedModel extends AbstractModel<M extends InterpolatedModel<A,B,M>> implements Serializable
 
 serialVersionUID:
 
 6174301903574154605L
 - Serialized Fields
 - a
```
Model<M extends Model<M>> a
```
 - b
```
Model<M extends Model<M>> b
```
 - lambda
```
double lambda
```
 - l1
```
double l1
```
- Class mpicbg.models.InverseCoordinateTransformList extends Object implements Serializable
 
 serialVersionUID:
 
 -3077711542359109619L
 - Serialized Fields
 - transforms
```
List<E> transforms
```
- Class mpicbg.models.InverseCoordinateTransformMap2D extends Object implements Serializable
 
 serialVersionUID:
 
 6356069579515246368L
 - Serialized Fields
 - map
```
float[][] map
```
 target coordinates addressed interleaved as map[ row ][ 2 * column ] = x map[ row ][ 2 * column + 1 ] = y
 - width
```
int width
```
 - height
```
int height
```
- Class mpicbg.models.InvertibleConstantModel extends ConstantModel<A extends Model<A> & InvertibleCoordinateTransform,M extends InvertibleConstantModel<A,M>> implements Serializable
 
 serialVersionUID:
 
 -8772404418680698608L
- Class mpicbg.models.InvertibleCoordinateTransformList extends Object implements Serializable
 
 serialVersionUID:
 
 2139051181642287413L
 - Serialized Fields
 - transforms
```
List<E> transforms
```
- Class mpicbg.models.InvertibleInterpolatedModel extends InterpolatedModel<A extends Model<A> & InvertibleCoordinateTransform,B extends Model & InvertibleCoordinateTransform,M extends InvertibleInterpolatedModel<A,B,M>> implements Serializable
 
 serialVersionUID:
 
 -1800786784345843623L
- Class mpicbg.models.MovingLeastSquaresMesh extends TransformMesh implements Serializable
 
 serialVersionUID:
 
 -5933039703937785040L
 - Serialized Fields
 - pt
```
HashMap<K,V> pt
```
 Tiles are a collection of PointMatches that share a common transformation model. In this implementation, each tile has the size of the whole mesh. By this means, all tiles initially share the same reference frame/ coordinate system. PointMatches are used for two completely different things: 1. Being the vertices which span the mesh and are thus required to find the affine transform inside each of the triangles. The PointMatches in a, l and pt are meant to be these vertices of the mesh. 2. Being actual point correspondences that define the local rigid transformations of each "tile".
 - error
```
double error
```
 - modelClass
```
Class<T> modelClass
```
- Class mpicbg.models.MovingLeastSquaresTransform extends AbstractMovingLeastSquaresTransform implements Serializable
 
 serialVersionUID:
 
 -8566403075161793547L
 - Serialized Fields
 - matches
```
Set<E> matches
```
- Class mpicbg.models.MovingLeastSquaresTransform2 extends AbstractMovingLeastSquaresTransform implements Serializable
 
 serialVersionUID:
 
 -8809482252029606075L
 - Serialized Fields
 - p
```
float[][] p
```
 - q
```
float[][] q
```
 - w
```
float[] w
```
- Class mpicbg.models.NoninvertibleModelException extends Exception implements Serializable
 
 serialVersionUID:
 
 8790171367047404173L
- Class mpicbg.models.NotEnoughDataPointsException extends Exception implements Serializable
 
 serialVersionUID:
 
 492656623783477968L
- Class mpicbg.models.Point extends Object implements Serializable
 
 serialVersionUID:
 
 -5885773585629275552L
 - Serialized Fields
 - w
```
double[] w
```
 World coordinates
 - l
```
double[] l
```
 Local coordinates
- Class mpicbg.models.PointMatch extends Object implements Serializable
 
 serialVersionUID:
 
 -3943684962223800732L
 - Serialized Fields
 - strength
```
double strength
```
 - p1
```
Point p1
```
 - p2
```
Point p2
```
 - weights
```
double[] weights
```
 - weight
```
double weight
```
- Class mpicbg.models.PolynomialTransform2D extends Object implements Serializable
 
 serialVersionUID:
 
 1101543117241957329L
 - Serialized Fields
 - order
```
int order
```
 order of the polynomial transform
 - a
```
double[] a
```
 holds two coefficients for each polynomial coefficient, including 1 initialized at 0 order, i.e. translation, the order follows that specified at http://bishopw.loni.ucla.edu/AIR5/2Dnonlinear.html#polylist two times
 - polTerms
```
double[] polTerms
```
 register to hold all polynomial terms during applyInPlace following the order specified at http://bishopw.loni.ucla.edu/AIR5/2Dnonlinear.html#polylist excluding 1 because we want to avoid repeated multiplication with 1
- Class mpicbg.models.RigidModel2D extends AbstractAffineModel2D<RigidModel2D> implements Serializable
 
 serialVersionUID:
 
 294104229960804720L
 - Serialized Fields
 - cos
```
double cos
```
 - sin
```
double sin
```
 - tx
```
double tx
```
 - ty
```
double ty
```
 - itx
```
double itx
```
 - ity
```
double ity
```
- Class mpicbg.models.RigidModel3D extends AbstractAffineModel3D<RigidModel3D> implements Serializable
 
 serialVersionUID:
 
 4703083104338949996L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m03
```
double m03
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m13
```
double m13
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - m23
```
double m23
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - i02
```
double i02
```
 - i03
```
double i03
```
 - i10
```
double i10
```
 - i11
```
double i11
```
 - i12
```
double i12
```
 - i13
```
double i13
```
 - i20
```
double i20
```
 - i21
```
double i21
```
 - i22
```
double i22
```
 - i23
```
double i23
```
 - isInvertible
```
boolean isInvertible
```
- Class mpicbg.models.SimilarityModel2D extends AbstractAffineModel2D<SimilarityModel2D> implements Serializable
 
 serialVersionUID:
 
 -2002621576568975203L
 - Serialized Fields
 - scos
```
double scos
```
 - ssin
```
double ssin
```
 - tx
```
double tx
```
 - ty
```
double ty
```
 - iscos
```
double iscos
```
 - issin
```
double issin
```
 - itx
```
double itx
```
 - ity
```
double ity
```
- Class mpicbg.models.SimilarityModel3D extends AbstractAffineModel3D<SimilarityModel3D> implements Serializable
 
 serialVersionUID:
 
 5509363764217496393L
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m03
```
double m03
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m13
```
double m13
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - m23
```
double m23
```
 - i00
```
double i00
```
 - i01
```
double i01
```
 - i02
```
double i02
```
 - i03
```
double i03
```
 - i10
```
double i10
```
 - i11
```
double i11
```
 - i12
```
double i12
```
 - i13
```
double i13
```
 - i20
```
double i20
```
 - i21
```
double i21
```
 - i22
```
double i22
```
 - i23
```
double i23
```
 - N
```
double[][] N
```
 - isInvertible
```
boolean isInvertible
```
- Class mpicbg.models.Spring extends Object implements Serializable
 
 serialVersionUID:
 
 1901169757781308736L
 - Serialized Fields
 - length
```
double length
```
 - maxStretch
```
double maxStretch
```
 - weights
```
double[] weights
```
 - weight
```
double weight
```
- Class mpicbg.models.SpringMesh extends TransformMesh implements Serializable
 
 serialVersionUID:
 
 -7744869220563880920L
 - Serialized Fields
 - fixedVertices
```
HashSet<E> fixedVertices
```
 - vertices
```
ArrayList<E> vertices
```
 - vp
```
HashMap<K,V> vp
```
 - pv
```
HashMap<K,V> pv
```
 - apv
```
HashMap<K,V> apv
```
 - pva
```
HashMap<K,V> pva
```
 - force
```
double force
```
 - minForce
```
double minForce
```
 - maxForce
```
double maxForce
```
 - maxSpeed
```
double maxSpeed
```
 - damp
```
double damp
```
- Class mpicbg.models.Tile extends Object implements Serializable
 
 serialVersionUID:
 
 3715791741771321832L
 - Serialized Fields
 - model
```
Model<M extends Model<M>> model
```
 The transformation AbstractModel of the Tile. All local Points in the Tile share (and thus determine) this common AbstractModel.
 - matches
```
Set<E> matches
```
 A set of point correspondences with p1 being a local point in this Tile and p2 being the corresponding local point in another Tile. Tiles are perfectly registered if both p1 and p1 have the same world coordinates for all PointMatches.
 - connectedTiles
```
Set<E> connectedTiles
```
 A set of Tiles that share point correpondences with this Tile. Note that point correspondences do not know about the tiles they belong to.
 - cost
```
double cost
```
 The transfer error of this Tile's AbstractModel as estimated from weighted square point correspondence displacement.
 - distance
```
double distance
```
 The average PointMatch displacement.
- Class mpicbg.models.TileConfiguration extends Object implements Serializable
 
 serialVersionUID:
 
 -5684886132202549487L
 - Serialized Fields
 - tiles
```
HashSet<E> tiles
```
 - fixedTiles
```
HashSet<E> fixedTiles
```
 - minError
```
double minError
```
 - maxError
```
double maxError
```
 - error
```
double error
```
- Class mpicbg.models.TransformMesh extends Object implements Serializable
 
 serialVersionUID:
 
 2557331683355356863L
 - Serialized Fields
 - width
```
double width
```
 - height
```
double height
```
 - av
```
HashMap<K,V> av
```
 - va
```
HashMap<K,V> va
```
- Class mpicbg.models.TransformMeshMap2D extends CoordinateTransformMap2D implements Serializable
 
 serialVersionUID:
 
 224883558672239029L
- Class mpicbg.models.TranslationModel1D extends AbstractAffineModel1D<TranslationModel1D> implements Serializable
 
 serialVersionUID:
 
 846402044582557842L
 - Serialized Fields
 - t
```
double t
```
- Class mpicbg.models.TranslationModel2D extends AbstractAffineModel2D<TranslationModel2D> implements Serializable
 
 serialVersionUID:
 
 -6412303652902075611L
 - Serialized Fields
 - tx
```
double tx
```
 - ty
```
double ty
```
- Class mpicbg.models.TranslationModel3D extends AbstractAffineModel3D<TranslationModel3D> implements Serializable
 
 serialVersionUID:
 
 2917354712492515946L
 - Serialized Fields
 - translation
```
double[] translation
```
- Class mpicbg.models.Vertex extends Point implements Serializable
 - Serialized Fields
 - springs
```
HashMap<K,V> springs
```
 A set of Springs.
 - direction
```
double[] direction
```
 The current moving direction of the Vertex. The length of this vector gives the current speed.
 - speed
```
double speed
```
 - forceSum
```
double forceSum
```
 The sum of all forces amplitudes applied to this Vertex.
 - force
```
double[] force
```
 The resulting force amplitude applied to this Vertex.
 - forceAmplitude
```
double forceAmplitude
```
Package mpicbg.panorama
- Class mpicbg.panorama.EquirectangularProjection extends PanoramaCamera<EquirectangularProjection> implements Serializable
 - Serialized Fields
 - lambdaPiScale
```
double lambdaPiScale
```
 - phiPiScale
```
double phiPiScale
```
 - minLambda
```
double minLambda
```
 - minPhi
```
double minPhi
```
- Class mpicbg.panorama.PanoramaCamera extends Object implements Serializable
 - Serialized Fields
 - m
```
Matrix3x3 m
```
 - i
```
Matrix3x3 i
```
 - f
```
double f
```
 - targetMaxSize
```
double targetMaxSize
```
 - targetWidth
```
double targetWidth
```
 - targetWidth2
```
double targetWidth2
```
 - targetHeight
```
double targetHeight
```
 - targetHeight2
```
double targetHeight2
```
- Class mpicbg.panorama.RectlinearCamera extends PanoramaCamera<RectlinearCamera> implements Serializable
 - Serialized Fields
 - sourceMaxSize
```
double sourceMaxSize
```
 - sourceWidth
```
double sourceWidth
```
 - sourceWidth2
```
double sourceWidth2
```
 - sourceHeight
```
double sourceHeight
```
 - sourceHeight2
```
double sourceHeight2
```
Package mpicbg.pointdescriptor
- Class mpicbg.pointdescriptor.LinkedPoint extends Point implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - link
```
Object link
```
Package mpicbg.pointdescriptor.exception
- Class mpicbg.pointdescriptor.exception.NoSuitablePointsException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package mpicbg.pointdescriptor.model
- Class mpicbg.pointdescriptor.model.FixedModel extends TranslationInvariantModel<FixedModel> implements Serializable
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m03
```
double m03
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m13
```
double m13
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - m23
```
double m23
```
- Class mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D extends TranslationInvariantModel<TranslationInvariantAffineModel3D> implements Serializable
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
- Class mpicbg.pointdescriptor.model.TranslationInvariantFixedModel extends TranslationInvariantModel<TranslationInvariantFixedModel> implements Serializable
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
- Class mpicbg.pointdescriptor.model.TranslationInvariantModel extends AbstractModel<M extends TranslationInvariantModel<M>> implements Serializable
- Class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D extends TranslationInvariantModel<TranslationInvariantRigidModel2D> implements Serializable
 - Serialized Fields
 - cos
```
double cos
```
 - sin
```
double sin
```
 - itx
```
double itx
```
 - ity
```
double ity
```
- Class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D extends TranslationInvariantModel<TranslationInvariantRigidModel3D> implements Serializable
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - N
```
double[][] N
```
- Class mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D extends TranslationInvariantModel<TranslationInvariantSimilarityModel3D> implements Serializable
 - Serialized Fields
 - m00
```
double m00
```
 - m01
```
double m01
```
 - m02
```
double m02
```
 - m10
```
double m10
```
 - m11
```
double m11
```
 - m12
```
double m12
```
 - m20
```
double m20
```
 - m21
```
double m21
```
 - m22
```
double m22
```
 - N
```
double[][] N
```
Package mpicbg.pointdescriptor.test
- Class mpicbg.pointdescriptor.test.PointNode extends Point implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - numDimensions
```
int numDimensions
```
Package mpicbg.spim.data
- Class mpicbg.spim.data.SpimDataException extends Exception implements Serializable
  
  serialVersionUID:
  
  8461622263661575411L
- Class mpicbg.spim.data.SpimDataInstantiationException extends SpimDataException implements Serializable
  
  serialVersionUID:
  
  8461622263661575411L
- Class mpicbg.spim.data.SpimDataIOException extends SpimDataException implements Serializable
  
  serialVersionUID:
  
  -7306608713023295089L
Package mpicbg.spim.io
- Class mpicbg.spim.io.ConfigurationParserException extends Exception implements Serializable
  
  serialVersionUID:
  
  1200597100039854833L
Package mpicbg.spim.mpicbg
- Class mpicbg.spim.mpicbg.PointMatchGeneric extends PointMatch implements Serializable
 
 serialVersionUID:
 
 1L
- Class mpicbg.spim.mpicbg.TileConfigurationPhaseCorrelation extends TileConfiguration implements Serializable
 - Serialized Fields
 - debugLevel
```
int debugLevel
```
- Class mpicbg.spim.mpicbg.TileSPIM extends Tile<M extends AbstractAffineModel3D<M>> implements Serializable
 - Serialized Fields
 - parent
```
ViewDataBeads parent
```
Package mpicbg.spim.registration.bead
- Class mpicbg.spim.registration.bead.Bead extends DetectionView<BeadIdentification,Bead> implements Serializable
 
 serialVersionUID:
 
 -2875282502611466531L
 - Serialized Fields
 - relocalized
```
boolean relocalized
```
Package mpicbg.spim.registration.detection
- Class mpicbg.spim.registration.detection.AbstractDetection extends Point implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - id
```
long id
```
 - weight
```
double weight
```
 - useW
```
boolean useW
```
 - distance
```
double distance
```
 - isUsed
```
boolean isUsed
```
- Class mpicbg.spim.registration.detection.Detection extends AbstractDetection<Detection> implements Serializable
 
 serialVersionUID:
 
 1L
- Class mpicbg.spim.registration.detection.DetectionView extends AbstractDetection<T extends DetectionView<S,T>> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - myView
```
ViewDataBeads myView
```
 - descriptorCorrespondence
```
ArrayList<E> descriptorCorrespondence
```
 - ransacCorrespondence
```
ArrayList<E> ransacCorrespondence
```
 - icpCorrespondence
```
ArrayList<E> icpCorrespondence
```
Package mpicbg.spim.registration.segmentation
- Class mpicbg.spim.registration.segmentation.Nucleus extends DetectionView<NucleusIdentification,Nucleus> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - weight
```
double weight
```
 - diameter
```
double diameter
```
 - assignedObject
```
Object assignedObject
```
 - isTrueCorrespondence
```
boolean isTrueCorrespondence
```
 - isFalseCorrespondence
```
boolean isFalseCorrespondence
```
 - isAmbigous
```
boolean isAmbigous
```
 - isUnique
```
boolean isUnique
```
 - numCorr
```
int numCorr
```
Package mpicbg.stitching
- Class mpicbg.stitching.ImagePlusTimePoint extends Tile implements Serializable
 - Serialized Fields
 - imp
```
ij.ImagePlus imp
```
 - impId
```
int impId
```
 - timePoint
```
int timePoint
```
 - dimensionality
```
int dimensionality
```
 - element
```
ImageCollectionElement element
```
- Class mpicbg.stitching.PointMatchStitching extends PointMatch implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - pair
```
ComparePair pair
```
- Class mpicbg.stitching.TileConfigurationStitching extends TileConfiguration implements Serializable
 - Serialized Fields
 - worstTile
```
Tile<M extends Model<M>> worstTile
```
Package mpicbg.trakem2.align
- Class mpicbg.trakem2.align.AbstractAffineTile2D extends Tile<A extends Model<A> & Affine2D<A>> implements Serializable
 
 serialVersionUID:
 
 -2229469138975635535L
 - Serialized Fields
 - patch
```
Patch patch
```
 - virtualMatches
```
Set<E> virtualMatches
```
 A set of virtual point correspondences that are used to connect a tile to the rest of the TileConfiguration assuming that the initial layout was correct. Virtual point correspondences are also stored in matches. This is just to keep track about them. Virtual point correspondences have to be removed for real connections. TODO Not yet tested---Do we need these virtual connections?
- Class mpicbg.trakem2.align.AbstractLayerAlignmentParam extends Object implements Serializable
 
 serialVersionUID:
 
 4186011617208423197L
 - Serialized Fields
 - ppm
```
AlignmentUtils.ParamPointMatch ppm
```
 - maxEpsilon
```
float maxEpsilon
```
 Maximal accepted alignment error in px
 - minInlierRatio
```
float minInlierRatio
```
 Inlier/candidates ratio
 - minNumInliers
```
int minNumInliers
```
 Minimal absolute number of inliers
 - expectedModelIndex
```
int expectedModelIndex
```
 - multipleHypotheses
```
boolean multipleHypotheses
```
 - widestSetOnly
```
boolean widestSetOnly
```
 - rejectIdentity
```
boolean rejectIdentity
```
 Ignore identity transform up to a given tolerance
 - identityTolerance
```
float identityTolerance
```
 - maxNumNeighbors
```
int maxNumNeighbors
```
 Maximal number of consecutive sections to be tested for an alignment model
 - maxNumFailures
```
int maxNumFailures
```
 Maximal number of consecutive slices for which no model could be found
 - desiredModelIndex
```
int desiredModelIndex
```
 - maxIterationsOptimize
```
int maxIterationsOptimize
```
 - maxPlateauwidthOptimize
```
int maxPlateauwidthOptimize
```
 - visualize
```
boolean visualize
```
 - maxNumThreads
```
int maxNumThreads
```
- Class mpicbg.trakem2.align.AffineTile2D extends AbstractAffineTile2D<AffineModel2D> implements Serializable
 
 serialVersionUID:
 
 -6891778987703462049L
- Class mpicbg.trakem2.align.Align.Param extends Object implements Serializable
 
 serialVersionUID:
 
 -6469820142091971052L
 - Serialized Fields
 - sift
```
FloatArray2DSIFT.Param sift
```
 - rod
```
float rod
```
 Closest/next closest neighbour distance ratio
 - maxEpsilon
```
float maxEpsilon
```
 Maximal allowed alignment error in px
 - minInlierRatio
```
float minInlierRatio
```
 Inlier/candidates ratio
 - minNumInliers
```
int minNumInliers
```
 Minimal absolute number of inliers
 - expectedModelIndex
```
int expectedModelIndex
```
 - desiredModelIndex
```
int desiredModelIndex
```
 - regularizerModelIndex
```
int regularizerModelIndex
```
 - regularize
```
boolean regularize
```
 Use a regularized model instead of a pure one.
 - lambda
```
double lambda
```
 Regularization weight.
 - correspondenceWeight
```
float correspondenceWeight
```
 - rejectIdentity
```
boolean rejectIdentity
```
 Ignore identity transform up to a given tolerance
 - identityTolerance
```
float identityTolerance
```
- Class mpicbg.trakem2.align.Align.ParamOptimize extends Align.Param implements Serializable
 
 serialVersionUID:
 
 2173278806083343006L
 - Serialized Fields
 - maxIterations
```
int maxIterations
```
 Maximal number of iteration allowed for the optimizer.
 - maxPlateauwidth
```
int maxPlateauwidth
```
 Maximal number of iterations allowed to not change the parameter to be optimized.
 - filterOutliers
```
boolean filterOutliers
```
 Filter outliers
 - meanFactor
```
float meanFactor
```
- Class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch extends Object implements Serializable
 
 serialVersionUID:
 
 7526084042028501775L
 - Serialized Fields
 - sift
```
FloatArray2DSIFT.Param sift
```
 - rod
```
float rod
```
 Closest/next closest neighbor distance ratio
 - clearCache
```
boolean clearCache
```
 - maxNumThreadsSift
```
int maxNumThreadsSift
```
- Class mpicbg.trakem2.align.ElasticLayerAlignment.Param extends AbstractLayerAlignmentParam implements Serializable
 
 serialVersionUID:
 
 208742614581106404L
 - Serialized Fields
 - isAligned
```
boolean isAligned
```
 - layerScale
```
double layerScale
```
 - minR
```
float minR
```
 - maxCurvatureR
```
float maxCurvatureR
```
 - rodR
```
float rodR
```
 - searchRadius
```
int searchRadius
```
 - blockRadius
```
int blockRadius
```
 - useLocalSmoothnessFilter
```
boolean useLocalSmoothnessFilter
```
 - localModelIndex
```
int localModelIndex
```
 - localRegionSigma
```
float localRegionSigma
```
 - maxLocalEpsilon
```
float maxLocalEpsilon
```
 - maxLocalTrust
```
float maxLocalTrust
```
 - resolutionSpringMesh
```
int resolutionSpringMesh
```
 - stiffnessSpringMesh
```
double stiffnessSpringMesh
```
 - dampSpringMesh
```
double dampSpringMesh
```
 - maxStretchSpringMesh
```
double maxStretchSpringMesh
```
 - maxIterationsSpringMesh
```
int maxIterationsSpringMesh
```
 - maxPlateauwidthSpringMesh
```
int maxPlateauwidthSpringMesh
```
 - useLegacyOptimizer
```
boolean useLegacyOptimizer
```
 - useTps
```
boolean useTps
```
- Class mpicbg.trakem2.align.ElasticMontage.Param extends Object implements Serializable
 
 serialVersionUID:
 
 8017492269521223930L
 - Serialized Fields
 - po
```
Align.ParamOptimize po
```
 - isAligned
```
boolean isAligned
```
 - tilesAreInPlace
```
boolean tilesAreInPlace
```
 - bmScale
```
double bmScale
```
 Block matching
 - bmMinR
```
float bmMinR
```
 - bmMaxCurvatureR
```
float bmMaxCurvatureR
```
 - bmRodR
```
float bmRodR
```
 - bmSearchRadius
```
int bmSearchRadius
```
 - bmBlockRadius
```
int bmBlockRadius
```
 - bmUseLocalSmoothnessFilter
```
boolean bmUseLocalSmoothnessFilter
```
 - bmLocalModelIndex
```
int bmLocalModelIndex
```
 - bmLocalRegionSigma
```
float bmLocalRegionSigma
```
 - bmMaxLocalEpsilon
```
float bmMaxLocalEpsilon
```
 - bmMaxLocalTrust
```
float bmMaxLocalTrust
```
 - springLengthSpringMesh
```
double springLengthSpringMesh
```
 Spring mesh
 - stiffnessSpringMesh
```
double stiffnessSpringMesh
```
 - dampSpringMesh
```
double dampSpringMesh
```
 - maxStretchSpringMesh
```
double maxStretchSpringMesh
```
 - maxIterationsSpringMesh
```
int maxIterationsSpringMesh
```
 - maxPlateauwidthSpringMesh
```
int maxPlateauwidthSpringMesh
```
 - useLegacyOptimizer
```
boolean useLegacyOptimizer
```
 - visualize
```
boolean visualize
```
 Visualize spring mesh optimization
 - maxNumThreads
```
int maxNumThreads
```
 Change this in case you want to limit the number of parallel threads to a specific number.
- Class mpicbg.trakem2.align.GenericAffineTile2D extends AbstractAffineTile2D<A extends Model<A> & Affine2D<A>> implements Serializable
 
 serialVersionUID:
 
 5632120826192026830L
- Class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param extends AbstractLayerAlignmentParam implements Serializable
 - Serialized Fields
 - regularize
```
boolean regularize
```
 Regularization
 - regularizerIndex
```
int regularizerIndex
```
 - lambda
```
double lambda
```
- Class mpicbg.trakem2.align.RigidTile2D extends AbstractAffineTile2D<RigidModel2D> implements Serializable
- Class mpicbg.trakem2.align.SimilarityTile2D extends AbstractAffineTile2D<SimilarityModel2D> implements Serializable
- Class mpicbg.trakem2.align.TileConfiguration extends TileConfiguration implements Serializable
- Class mpicbg.trakem2.align.TranslationTile2D extends AbstractAffineTile2D<TranslationModel2D> implements Serializable
- Class mpicbg.trakem2.align.Util.Features extends Object implements Serializable
 
 serialVersionUID:
 
 -5707602842402593215L
 - Serialized Fields
 - key
```
Object key
```
 - features
```
ArrayList<E> features
```
- Class mpicbg.trakem2.align.Util.PointMatches extends Object implements Serializable
 
 serialVersionUID:
 
 7905488521562090982L
 - Serialized Fields
 - key
```
Object key
```
 - pointMatches
```
ArrayList<E> pointMatches
```
Package mpicbg.trakem2.align.concurrent
- Class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable extends Object implements Serializable
 - Serialized Fields
 - layer1
```
Layer layer1
```
 - layer2
```
Layer layer2
```
 - layer1Fixed
```
boolean layer1Fixed
```
 - layer2Fixed
```
boolean layer2Fixed
```
 - filter
```
Filter<T> filter
```
 - param
```
ElasticLayerAlignment.Param param
```
 - v1
```
Collection<E> v1
```
 - v2
```
Collection<E> v2
```
 - box
```
Rectangle box
```
 - pair
```
Triple<A,B,C> pair
```
- Class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults extends Object implements Serializable
 - Serialized Fields
 - v1
```
Collection<E> v1
```
 - v2
```
Collection<E> v2
```
 - pm12
```
Collection<E> pm12
```
 - pm21
```
Collection<E> pm21
```
 - layer1Fixed
```
boolean layer1Fixed
```
 - layer2Fixed
```
boolean layer2Fixed
```
 - pair
```
Triple<A,B,C> pair
```
Package mpicbg.trakem2.transform
- Class mpicbg.trakem2.transform.AffineModel2D extends AffineModel2D implements Serializable
 
 serialVersionUID:
 
 7177056267150312600L
- Class mpicbg.trakem2.transform.AffineModel3D extends AffineModel3D implements Serializable
 
 serialVersionUID:
 
 4661684107044575726L
- Class mpicbg.trakem2.transform.CoordinateTransformList extends CoordinateTransformList<E extends CoordinateTransform> implements Serializable
 
 serialVersionUID:
 
 8134060157022268181L
- Class mpicbg.trakem2.transform.HomographyModel2D extends HomographyModel2D implements Serializable
 
 serialVersionUID:
 
 3098424136915475353L
- Class mpicbg.trakem2.transform.InvertibleCoordinateTransformList extends InvertibleCoordinateTransformList<E extends InvertibleCoordinateTransform> implements Serializable
 
 serialVersionUID:
 
 8609337486676867142L
- Class mpicbg.trakem2.transform.MovingLeastSquaresTransform extends MovingLeastSquaresTransform implements Serializable
 
 serialVersionUID:
 
 969438449108820224L
- Class mpicbg.trakem2.transform.MovingLeastSquaresTransform2 extends MovingLeastSquaresTransform2 implements Serializable
 
 serialVersionUID:
 
 4878940232249133983L
- Class mpicbg.trakem2.transform.NonLinearCoordinateTransform extends Object implements Serializable
 - Serialized Fields
 - beta
```
double[][] beta
```
 - normMean
```
double[] normMean
```
 - normVar
```
double[] normVar
```
 - dimension
```
int dimension
```
 - length
```
int length
```
 - width
```
int width
```
 - height
```
int height
```
- Class mpicbg.trakem2.transform.PolynomialTransform2D extends PolynomialTransform2D implements Serializable
 
 serialVersionUID:
 
 -3905373956331925743L
- Class mpicbg.trakem2.transform.RigidModel2D extends RigidModel2D implements Serializable
- Class mpicbg.trakem2.transform.SimilarityModel2D extends SimilarityModel2D implements Serializable
- Class mpicbg.trakem2.transform.ThinPlateSplineTransform extends Object implements Serializable
 
 serialVersionUID:
 
 2214564089916179653L
 - Serialized Fields
 - tps
```
ThinPlateR2LogRSplineKernelTransform tps
```
- Class mpicbg.trakem2.transform.TransformMesh extends TransformMesh implements Serializable
 - Serialized Fields
 - boundingBox
```
Rectangle boundingBox
```
- Class mpicbg.trakem2.transform.TranslationModel2D extends TranslationModel2D implements Serializable
- Class mpicbg.trakem2.transform.TranslationModel3D extends TranslationModel3D implements Serializable
Package mpicbg.trakem2.util
- Class mpicbg.trakem2.util.Triple extends Object implements Serializable
  - Serialized Fields
    - a
```
Object a
```
    - b
```
Object b
```
    - c
```
Object c
```
Package mpicbg.util
- Class mpicbg.util.Matrix3x3 extends Object implements Serializable
  
  serialVersionUID:
  
  -6777226221195033854L
  - Serialized Fields
    - m00
```
double m00
```
    - m01
```
double m01
```
    - m02
```
double m02
```
    - m10
```
double m10
```
    - m11
```
double m11
```
    - m12
```
double m12
```
    - m20
```
double m20
```
    - m21
```
double m21
```
    - m22
```
double m22
```

Package net.imagej.ui.swing.ops

Class net.imagej.ui.swing.ops.OpFinder extends JFrame implements Serializable

Serialized Fields

simple
```
boolean simple
```

modeButton

net.imagej.ui.swing.ops.OpFinder.ModeButton modeButton

searchLabel
```
JLabel searchLabel
```
autoToggle
```
boolean autoToggle
```
simpleFilterClasses
```
Set<E> simpleFilterClasses
```

lastFilter

net.imagej.ui.swing.ops.OpFinder.FilterRunner lastFilter

lastHTMLReq

net.imagej.ui.swing.ops.OpFinder.HTMLFetcher lastHTMLReq

widths
```
int[] widths
```
searchField
```
JTextField searchField
```

treeTable

org.jdesktop.swingx.JXTreeTable treeTable

successLabel
```
JLabel successLabel
```
textPane
```
JEditorPane textPane
```
detailsPane
```
JScrollPane detailsPane
```
toggleDetailsButton
```
JButton toggleDetailsButton
```
mainPane
```
JPanel mainPane
```
splitPane
```
JSplitPane splitPane
```
progressBar
```
JProgressBar progressBar
```
advModel
```
OpTreeTableModel advModel
```
smplModel
```
OpTreeTableModel smplModel
```
opFail
```
ImageIcon opFail
```
opSuccess
```
ImageIcon opSuccess
```
expandDetails
```
ImageIcon expandDetails
```
hideDetails
```
ImageIcon hideDetails
```
useView
```
ImageIcon useView
```
devView
```
ImageIcon devView
```
advExpandedPaths
```
Set<E> advExpandedPaths
```
smplExpandedPaths
```
Set<E> smplExpandedPaths
```
elementsMap
```
Map<K,V> elementsMap
```
advTries
```
Map<K,V> advTries
```
smplTries
```
Map<K,V> smplTries
```
successTimer
```
Timer successTimer
```
progressTimer
```
Timer progressTimer
```
opService
```
OpService opService
```
prefService
```
PrefService prefService
```
logService
```
LogService logService
```
platformService
```
PlatformService platformService
```
scriptService
```
ScriptService scriptService
```
threadService
```
ThreadService threadService
```

Package oldsegmenters
- Class oldsegmenters.Segmentator_ extends JFrame implements Serializable
 - Serialized Fields
 - labelList
```
JList<E> labelList
```
 - labelListModel
```
DefaultListModel<E> labelListModel
```
 - minThreshold
```
JSpinner minThreshold
```
 - maxThreshold
```
JSpinner maxThreshold
```
 - autoLabelFileLoc
```
JTextField autoLabelFileLoc
```
- Class oldsegmenters.Segmenter_ extends JFrame implements Serializable
 - Serialized Fields
 - labelList
```
JList<E> labelList
```
 - labelListModel
```
DefaultListModel<E> labelListModel
```
 - minThreshold
```
JSpinner minThreshold
```
 - maxThreshold
```
JSpinner maxThreshold
```
 - markingLabel
```
JLabel markingLabel
```

Package org.imagearchive.lsm.toolbox.gui

Class org.imagearchive.lsm.toolbox.gui.AboutDialog extends JDialog implements Serializable

Serialized Fields

masterModel
```
MasterModel masterModel
```
about
```
JEditorPane about
```
changelog
```
JEditorPane changelog
```
iconset
```
JEditorPane iconset
```
license
```
JEditorPane license
```
help
```
JEditorPane help
```
aboutScroller
```
JScrollPane aboutScroller
```
changelogScroller
```
JScrollPane changelogScroller
```
helpScroller
```
JScrollPane helpScroller
```
licenseScroller
```
JScrollPane licenseScroller
```
iconsetScroller
```
JScrollPane iconsetScroller
```
tabber
```
JTabbedPane tabber
```
okButton
```
JButton okButton
```
ScreenDimension
```
Dimension ScreenDimension
```
ScreenX
```
int ScreenX
```
ScreenY
```
int ScreenY
```
infoTitle
```
JLabel infoTitle
```
infoText
```
String infoText
```

Class org.imagearchive.lsm.toolbox.gui.BatchDialog extends JDialog implements Serializable

Serialized Fields

okButton
```
JButton okButton
```
cancelButton
```
JButton cancelButton
```
masterModel
```
MasterModel masterModel
```
title
```
String title
```
buttonsPanel
```
JPanel buttonsPanel
```
mainPanel
```
JPanel mainPanel
```
sourceLabel
```
JLabel sourceLabel
```
outputLabel
```
JLabel outputLabel
```
formatLabel
```
JLabel formatLabel
```
sourceTable
```
JTable sourceTable
```
sourcePane
```
JScrollPane sourcePane
```
outputTF
```
JTextField outputTF
```
sourceButton
```
JButton sourceButton
```
outputButton
```
JButton outputButton
```
resetButton
```
JButton resetButton
```
formatCombo
```
JComboBox<E> formatCombo
```
verboseCB
```
JCheckBox verboseCB
```
dirCB
```
JCheckBox dirCB
```
parent
```
JFrame parent
```

Class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame extends JFrame implements Serializable

Serialized Fields

infoFrame
```
InfoFrame infoFrame
```
pan
```
JPanel pan
```
gridBagLayout
```
GridBagLayout gridBagLayout
```
openLSMButton
```
GUIButton openLSMButton
```
closeWindowsButton
```
GUIButton closeWindowsButton
```
exitButton
```
GUIButton exitButton
```
showInfoButton
```
GUIButton showInfoButton
```
browseButton
```
GUIButton browseButton
```
fmButton
```
GUIButton fmButton
```
applyStampButton
```
GUIButton applyStampButton
```
applyTStampItem
```
GUIMenuItem applyTStampItem
```
applyZStampItem
```
GUIMenuItem applyZStampItem
```
applyLStampItem
```
GUIMenuItem applyLStampItem
```
editPaletteButton
```
GUIButton editPaletteButton
```
batchConvertButton
```
GUIButton batchConvertButton
```
helpButton
```
GUIButton helpButton
```
macroButton
```
GUIButton macroButton
```
rbButton
```
JToggleButton rbButton
```
title
```
String title
```
titleLabel
```
JLabel titleLabel
```
stampsPM
```
JPopupMenu stampsPM
```
hyperVolumePM
```
JPopupMenu hyperVolumePM
```
fmPM
```
JPopupMenu fmPM
```
hyperVolumeItem
```
JMenuItem hyperVolumeItem
```
image5DItem
```
JMenuItem image5DItem
```
fuseItem
```
JMenuItem fuseItem
```
mergeItem
```
JMenuItem mergeItem
```
LSMinfoText
```
String[] LSMinfoText
```
timestamps_count
```
long timestamps_count
```
ScreenDimension
```
Dimension ScreenDimension
```
ScreenX
```
int ScreenX
```
ScreenY
```
int ScreenY
```
baseFrameXlocation
```
int baseFrameXlocation
```
baseFrameYlocation
```
int baseFrameYlocation
```
selectedToolBarButtonID
```
int selectedToolBarButtonID
```
masterModel
```
MasterModel masterModel
```

Class org.imagearchive.lsm.toolbox.gui.DetailsFrame extends JFrame implements Serializable

Serialized Fields

masterModel
```
MasterModel masterModel
```
detailsFrameXsize
```
int detailsFrameXsize
```
detailsFrameYsize
```
int detailsFrameYsize
```
detailsFrameXlocation
```
int detailsFrameXlocation
```
detailsFrameYlocation
```
int detailsFrameYlocation
```
detailsTree
```
JTree detailsTree
```
table
```
JTable table
```
toolBar
```
JToolBar toolBar
```
exitButton
```
JButton exitButton
```
dumpButton
```
JButton dumpButton
```
xmlButton
```
JButton xmlButton
```
filterButton
```
JToggleButton filterButton
```
searchButton
```
JButton searchButton
```
searchTF
```
JTextField searchTF
```
treemodel
```
DefaultTreeModel treemodel
```

tablemodel

org.imagearchive.lsm.toolbox.gui.TreeTableModel tablemodel

expandAllItem
```
JMenuItem expandAllItem
```
collapseAllItem
```
JMenuItem collapseAllItem
```
filterCBItem
```
JCheckBoxMenuItem filterCBItem
```
detailsTreePopupMenu
```
JPopupMenu detailsTreePopupMenu
```
frameTitle
```
String frameTitle
```
title
```
String title
```
lastNodeResult
```
DefaultMutableTreeNode lastNodeResult
```
searchCoordinates
```
Point searchCoordinates
```
lsm
```
LSMFileInfo lsm
```

Class org.imagearchive.lsm.toolbox.gui.GUIButton extends JButton implements Serializable
Class org.imagearchive.lsm.toolbox.gui.GUIMenuItem extends JMenuItem implements Serializable
Class org.imagearchive.lsm.toolbox.gui.ImagePreview extends JPanel implements Serializable
- Serialized Fields
  - thumbnail
```
ImageIcon thumbnail
```
  - imp
```
ij.ImagePlus imp
```
  - slider
```
JSlider slider
```
  - file
```
File file
```
  - reader
```
Reader reader
```
  - panel
```
JPanel panel
```
  - backgroundcolor
```
Color backgroundcolor
```
Class org.imagearchive.lsm.toolbox.gui.InfoFrame extends JFrame implements Serializable
- Serialized Fields
  - masterModel
```
MasterModel masterModel
```
  - detailsFrame
```
DetailsFrame detailsFrame
```
  - notesDialog
```
NotesDialog notesDialog
```
  - infoFrameXsize
```
int infoFrameXsize
```
  - infoFrameYsize
```
int infoFrameYsize
```
  - infolab
```
JLabel[] infolab
```
  - area
```
JTextArea[] area
```
Class org.imagearchive.lsm.toolbox.gui.InfoNode extends DefaultMutableTreeNode implements Serializable
- Serialized Fields
  - data
```
Object data
```
  - title
```
String title
```
Class org.imagearchive.lsm.toolbox.gui.LsmImageTableModel extends AbstractTableModel implements Serializable
- Serialized Fields
 - files
```
ArrayList<E> files
```
 - columnTitles
```
String[] columnTitles
```
Class org.imagearchive.lsm.toolbox.gui.NotesDialog extends JDialog implements Serializable
- Serialized Fields
  - tsnotes
```
JTextArea tsnotes
```
  - tdnotes
```
JTextArea tdnotes
```
  - panel
```
JPanel panel
```
  - masterModel
```
MasterModel masterModel
```
Class org.imagearchive.lsm.toolbox.gui.SelectImageDialog extends JDialog implements Serializable
- Serialized Fields
 - panel
```
JPanel panel
```
 - imageList
```
JList<E> imageList
```
 - masterModel
```
MasterModel masterModel
```
 - fileInfos
```
Vector<E> fileInfos
```
 - images
```
Vector<E> images
```
 - label
```
String label
```
 - okButton
```
JButton okButton
```
 - cancelButton
```
JButton cancelButton
```
 - returnVal
```
int returnVal
```
 - values
```
int[] values
```
 - channel
```
boolean channel
```

Package org.janelia.thickness.inference
- Class org.janelia.thickness.inference.Options extends Object implements Serializable
  
  serialVersionUID:
  
  3591334824905556420L
  - Serialized Fields
    - scalingFactorRegularizerWeight
```
Double scalingFactorRegularizerWeight
```
    - coordinateUpdateRegularizerWeight
```
Double coordinateUpdateRegularizerWeight
```
    - shiftProportion
```
Double shiftProportion
```
    - nIterations
```
Integer nIterations
```
    - comparisonRange
```
Integer comparisonRange
```
    - minimumSectionThickness
```
Double minimumSectionThickness
```
    - regularizationType
```
InferFromMatrix.RegularizationType regularizationType
```
    - scalingFactorEstimationIterations
```
Integer scalingFactorEstimationIterations
```
    - withReorder
```
Boolean withReorder
```
    - forceMonotonicity
```
Boolean forceMonotonicity
```
    - estimateWindowRadius
```
Integer estimateWindowRadius
```
    - minimumCorrelationValue
```
Double minimumCorrelationValue
```
Package org.janelia.thickness.plugin
- Class org.janelia.thickness.plugin.NonBlockingGenericDialogWithFileField extends NonBlockingGenericDialog implements Serializable
Package org.janelia.utility.ui
- Class org.janelia.utility.ui.RepeatingReleasedEventsFixer.RepostedKeyEvent extends KeyEvent implements Serializable
Package org.siox.example
- Class org.siox.example.ControlJPanel extends JPanel implements Serializable
 - Serialized Fields
 - applySelectionAction
```
Action applySelectionAction
```
 Action that applies the selection candiate.
 - startSioxAction
```
Action startSioxAction
```
 Action that performs the segmentation.
 - roiJPanel
```
JPanel roiJPanel
```
 - segJPanel
```
JPanel segJPanel
```
 - drbJPanel
```
JPanel drbJPanel
```
 - selectModeJLabel
```
JLabel selectModeJLabel
```
 - smoothJLabel
```
JLabel smoothJLabel
```
 - brushsizeJLabel
```
JLabel brushsizeJLabel
```
 - brushtypeJLabel
```
JLabel brushtypeJLabel
```
 - fgOrBgJLabel
```
JLabel fgOrBgJLabel
```
 - applyJButton
```
JButton applyJButton
```
 - segmentateJButton
```
JButton segmentateJButton
```
 - fgJRadioButton
```
JRadioButton fgJRadioButton
```
 - bgJRadioButton
```
JRadioButton bgJRadioButton
```
 - smoothness
```
JSlider smoothness
```
 - brushsize
```
JSlider brushsize
```
 - addThreshold
```
JSlider addThreshold
```
 - subThreshold
```
JSlider subThreshold
```
 - multipart
```
JCheckBox multipart
```
 - rectJRadioButton
```
JRadioButton rectJRadioButton
```
 - ellipJRadioButton
```
JRadioButton ellipJRadioButton
```
 - lassoJRadioButton
```
JRadioButton lassoJRadioButton
```
 - addJRadioButton
```
JRadioButton addJRadioButton
```
 - subJRadioButton
```
JRadioButton subJRadioButton
```
 - diskJRadioButton
```
JRadioButton diskJRadioButton
```
 - squareJRadioButton
```
JRadioButton squareJRadioButton
```
 - scrollDisplay
```
ScrollDisplay scrollDisplay
```
 - imageWindow
```
Component imageWindow
```
 - jDesktopPane
```
JDesktopPane jDesktopPane
```
 - arrayListOfWindowListener
```
ArrayList<E> arrayListOfWindowListener
```
 WindowListeners added to any image display dialog.
 - arrayListOfJifListener
```
ArrayList<E> arrayListOfJifListener
```
 InternalFrameListeners added to any internal frame with image display.
 - status
```
int status
```
 One of the status constants, denotes current processing step.
 - checkForUnsavedChanges
```
boolean checkForUnsavedChanges
```
 Should image displays be checked for unsaved changes before closing them?
- Class org.siox.example.ImagePane extends JComponent implements Serializable
 - Serialized Fields
 - origImage
```
BufferedImage origImage
```
 Local copy of original image, used for reset.
 - currImage
```
BufferedImage currImage
```
 Working instance of image.
 - iWidth
```
int iWidth
```
 Image dimension.
 - iHeight
```
int iHeight
```
 Image dimension.
 - tmpBuffer
```
int[] tmpBuffer
```
 Temporary ARGB arry for alpha blending operations on image.
 - selection
```
Shape selection
```
 Current selection, a Rectangle2D, a Ellipse2D, or a general path enclosing the current selection (lasso selection). Set to null when not visible.
 - selectionAnchor
```
Point2D selectionAnchor
```
 Start point of current selection.
 - unsavedChanges
```
boolean unsavedChanges
```
 Image has unsaved changes?
 - zoomFactor
```
int zoomFactor
```
 The scaling factor the image should be shown with, must be greater zero.
 - zoomIn
```
boolean zoomIn
```
 Scale up or scale down?
 - bgTileIcon
```
Icon bgTileIcon
```
 Background image tile as icon.
 - topIcon
```
Icon topIcon
```
 To be drawn next to image, if inner offset allows them to be lie fully within this component.
 - leftIcon
```
Icon leftIcon
```
 To be drawn next to image, if inner offset allows them to be lie fully within this component.
- Class org.siox.example.JRuler extends JComponent implements Serializable
 - Serialized Fields
 - scrollDisplay
```
ScrollDisplay scrollDisplay
```
 The display this is connected to.
 - sizeForMarks
```
int sizeForMarks
```
 Vertical size for horizontal rulers and vice versa.
 - rulerLength
```
int rulerLength
```
 Maximum entry of this ruler in pixel.
 - orientation
```
int orientation
```
 Orientation, HORIZONTAL or VERTICAL.
 - maxScale
```
int maxScale
```
 Maximum supported scale factor.
 - unitMode
```
int unitMode
```
 What unit to show.
- Class org.siox.example.Main extends JApplet implements Serializable
 - Serialized Fields
 - ctrlJPanel
```
ControlJPanel ctrlJPanel
```
 The user input managing control panel.
 - canWriteFiles
```
boolean canWriteFiles
```
 Permission flag for write files.
 - isInitedAsApplet
```
boolean isInitedAsApplet
```
 Flag set when inited as applet.
 - targetFile
```
File targetFile
```
 Currently save target, null for none.
 - openAction
```
Action openAction
```
 - openUrlAction
```
Action openUrlAction
```
 - saveAction
```
Action saveAction
```
 - saveAsAction
```
Action saveAsAction
```
 - resetAction
```
Action resetAction
```
 - zoomActions
```
Action[] zoomActions
```
 - bgActions
```
Action[] bgActions
```
 - rulerActions
```
Action[] rulerActions
```
 - zoomGroup
```
ButtonGroup zoomGroup
```
 - bgGroup
```
ButtonGroup bgGroup
```
 - rulerGroup
```
ButtonGroup rulerGroup
```
 - hashMapOfZooms
```
HashMap<K,V> hashMapOfZooms
```
 - hashMapOfBgs
```
HashMap<K,V> hashMapOfBgs
```
 - hashMapOfRulers
```
HashMap<K,V> hashMapOfRulers
```
- Class org.siox.example.ScrollDisplay extends JScrollPane implements Serializable
 - Serialized Fields
 - imagePane
```
ImagePane imagePane
```
 The image displaying panel inside this scroll pane.
 - siox
```
SioxSegmentator siox
```
 The segmentator to segmentate the image.
 - imgData
```
int[] imgData
```
 Pixel data of the image to be segmentated.
 - confMatrix
```
float[] confMatrix
```
 The confidence matrix that stores the segmentation result. A confidence of 0 means the pixel is background, a confidence of 1.0 means the pixel is foreground.
 - colJRuler
```
JRuler colJRuler
```
 Optional rulers as header component.
 - rowJRuler
```
JRuler rowJRuler
```
 Optional rulers as header component.
 - innerColJRuler
```
JRuler innerColJRuler
```
 Rulers used as icons in imagePane when image is smaller as imagePane.
 - innerRowJRuler
```
JRuler innerRowJRuler
```
 Rulers used as icons in imagePane when image is smaller as imagePane.
 - rulerMode
```
int rulerMode
```
 Ruler mode set.
Package pal.math
- Class pal.math.Binomial extends Object implements Serializable
  - Serialized Fields
    - nChoose2
```
double[] nChoose2
```
- Class pal.math.ConjugateDirectionSearch.OptimizationError extends RuntimeException implements Serializable
- Class pal.math.MersenneTwisterFast extends Object implements Serializable
  - Serialized Fields
    - mt
```
int[] mt
```
    - mti
```
int mti
```
    - mag01
```
int[] mag01
```
    - nextNextGaussian
```
double nextNextGaussian
```
    - haveNextNextGaussian
```
boolean haveNextNextGaussian
```
- Class pal.math.UrnModel extends Object implements Serializable
  - Serialized Fields
    - capacity
```
int capacity
```
    - numNumbers
```
int numNumbers
```
    - numDrawn
```
int numDrawn
```
    - next
```
int next
```
    - isAvailable
```
boolean[] isAvailable
```
    - rng
```
MersenneTwisterFast rng
```
Package process
- Class process.Particle extends Point implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - id
```
int id
```
 - peak
```
DifferenceOfGaussianPeak<T extends NumericType<T>> peak
```
 - weight
```
double weight
```
 - distance
```
double distance
```
 - diameter
```
float diameter
```
 - zStretching
```
float zStretching
```
 - useW
```
boolean useW
```

Package sc.fiji.balloonSegmentation

Class sc.fiji.balloonSegmentation.BalloonSegmentation_ extends JFrame implements Serializable

Serialized Fields

bal1
```
Balloon bal1
```
fontMetrics
```
FontMetrics fontMetrics
```
PixelLevel
```
JSlider PixelLevel
```
mainLayout
```
BoxLayout mainLayout
```
pixelLayout
```
BoxLayout pixelLayout
```
ActionLayout
```
GridBagLayout ActionLayout
```
constraint
```
GridBagConstraints constraint
```
boundsLayout
```
GridLayout boundsLayout
```
centerLayout
```
GridLayout centerLayout
```
inflateLayout
```
GridLayout inflateLayout
```
resultsLayout
```
GridLayout resultsLayout
```
buttonsLayout
```
GridLayout buttonsLayout
```
bnBound
```
JButton bnBound
```
bnInflate
```
JButton bnInflate
```
bnRefine
```
JButton bnRefine
```
bnOptimize
```
JButton bnOptimize
```
bnClose
```
JButton bnClose
```
bnSample
```
JButton bnSample
```
bnFromROI
```
JButton bnFromROI
```
bnEdit
```
JToggleButton bnEdit
```
bnClear
```
JButton bnClear
```
bnShow
```
JButton bnShow
```
bnModify
```
JButton bnModify
```
bnOpen
```
JButton bnOpen
```
bnCapture
```
JButton bnCapture
```
txtPixLevel
```
JTextField txtPixLevel
```
txtRem
```
JTextField txtRem
```
txtHL
```
JTextField txtHL
```
txtCellID
```
JTextField txtCellID
```
txtIniLevel
```
JTextField txtIniLevel
```
txtEndLevel
```
JTextField txtEndLevel
```
ChkProcessAll1
```
Checkbox ChkProcessAll1
```
ChkProcessAll2
```
Checkbox ChkProcessAll2
```
chkLog
```
Checkbox chkLog
```
showOptionsList
```
JComboBox<E> showOptionsList
```
editOptionsList
```
JComboBox<E> editOptionsList
```
min_pix_level
```
int min_pix_level
```
max_pix_level
```
int max_pix_level
```

Package sc.fiji.cellCounter

Class sc.fiji.cellCounter.Cell_Counter extends ij.plugin.frame.PlugInFrame implements Serializable
Class sc.fiji.cellCounter.CellCntrImageCanvas extends ImageCanvas implements Serializable
- Serialized Fields
 - typeVector
```
Vector<E> typeVector
```
 - currentMarkerVector
```
CellCntrMarkerVector currentMarkerVector
```
 - cc
```
CellCounter cc
```
 - img
```
ij.ImagePlus img
```
 - delmode
```
boolean delmode
```
 - showNumbers
```
boolean showNumbers
```
 - showAll
```
boolean showAll
```
 - font
```
Font font
```
 - srcRect
```
Rectangle srcRect
```
Class sc.fiji.cellCounter.CellCntrMarkerVector extends Vector<CellCntrMarker> implements Serializable
- Serialized Fields
 - type
```
int type
```
 - name
```
String name
```

Class sc.fiji.cellCounter.CellCounter extends JFrame implements Serializable

Serialized Fields

typeVector
```
Vector<E> typeVector
```
dynRadioVector
```
Vector<E> dynRadioVector
```
txtFieldVector
```
Vector<E> txtFieldVector
```
markerVector
```
CellCntrMarkerVector markerVector
```

currentMarkerVector

CellCntrMarkerVector currentMarkerVector

currentMarkerIndex
```
int currentMarkerIndex
```
metaData
```
Map<K,V> metaData
```
dynPanel
```
JPanel dynPanel
```
dynButtonPanel
```
JPanel dynButtonPanel
```
statButtonPanel
```
JPanel statButtonPanel
```
dynTxtPanel
```
JPanel dynTxtPanel
```
delCheck
```
JCheckBox delCheck
```
newCheck
```
JCheckBox newCheck
```
numbersCheck
```
JCheckBox numbersCheck
```
showAllCheck
```
JCheckBox showAllCheck
```
radioGrp
```
ButtonGroup radioGrp
```
separator
```
JSeparator separator
```
addButton
```
JButton addButton
```
removeButton
```
JButton removeButton
```
renameButton
```
JButton renameButton
```
initializeButton
```
JButton initializeButton
```
optionsButton
```
JButton optionsButton
```
resultsButton
```
JButton resultsButton
```
deleteButton
```
JButton deleteButton
```
resetButton
```
JButton resetButton
```
exportButton
```
JButton exportButton
```
loadButton
```
JButton loadButton
```
exportimgButton
```
JButton exportimgButton
```
measureButton
```
JButton measureButton
```
keepOriginal
```
boolean keepOriginal
```
ic
```
CellCntrImageCanvas ic
```
img
```
ij.ImagePlus img
```
counterImg
```
ij.ImagePlus counterImg
```
dynGrid
```
GridLayout dynGrid
```

Package sc.fiji.coloc.algorithms
- Class sc.fiji.coloc.algorithms.MissingPreconditionException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L

Package sc.fiji.coloc.results

Class sc.fiji.coloc.results.SingleWindowDisplay extends JFrame implements Serializable

serialVersionUID:: -5642321584354176878L

Serialized Fields

displayOriginalImages
```
boolean displayOriginalImages
```

currentlyDisplayedImageResult

RandomAccessibleInterval<T> currentlyDisplayedImageResult

listOfImages
```
List<E> listOfImages
```
mapOf2DHistograms
```
Map<K,V> mapOf2DHistograms
```
warnings
```
List<E> warnings
```
valueResults
```
List<E> valueResults
```
listOfLUTs
```
Map<K,V> listOfLUTs
```
pixelAccessCursor
```
RandomAccess<T> pixelAccessCursor
```

pdfWriter

PDFWriter<T extends RealType<T>> pdfWriter

imp
```
ij.ImagePlus imp
```
imagePanel
```
JImagePanel imagePanel
```
listButton
```
JButton listButton
```
copyButton
```
JButton copyButton
```
log
```
JCheckBox log
```

dataContainer

DataContainer<T extends RealType<T>> dataContainer

Package sc.fiji.hdf5

Class sc.fiji.hdf5.HDF5_Reader_Vibez extends JFrame implements Serializable
- Serialized Fields
 - dataSets_
```
ArrayList<E> dataSets_
```
 - pathTable_
```
JTable pathTable_
```
 - fullFileName_
```
String fullFileName_
```
 - loadAsRadioButtons_
```
JRadioButton[] loadAsRadioButtons_
```
 - loadAsMode_
```
int loadAsMode_
```
 - nChannelsSpinner_
```
SpinnerNumberModel nChannelsSpinner_
```
 - dsetLayoutTextField_
```
JTextField dsetLayoutTextField_
```

Class sc.fiji.hdf5.HDF5_Writer_Vibez extends Frame implements Serializable

Serialized Fields

_filename
```
String _filename
```
_saveMode
```
String _saveMode
```
_imp
```
ij.ImagePlus _imp
```
_mylayout
```
BoxLayout _mylayout
```
_compressionSelect
```
JComboBox<E> _compressionSelect
```
_presetSelect
```
JComboBox<E> _presetSelect
```
_dsetNameTempl
```
JTextField _dsetNameTempl
```
_textAreaT
```
JTextArea _textAreaT
```
_textAreaC
```
JTextArea _textAreaC
```
_dsetNamesPreview
```
JLabel _dsetNamesPreview
```
_mappingPresets
```
ArrayList<E> _mappingPresets
```

Package sc.fiji.i5d.gui
- Class sc.fiji.i5d.gui.ChannelControl extends Panel implements Serializable
 
 serialVersionUID:
 
 -3537465383241321652L
 - Serialized Fields
 - win
```
Image5DWindow win
```
 - i5d
```
Image5D i5d
```
 - ij
```
ij.ImageJ ij
```
 - displayChoice
```
Choice displayChoice
```
 - displayMode
```
int displayMode
```
 - displayGrayInTiles
```
boolean displayGrayInTiles
```
 - selectorPanel
```
Panel selectorPanel
```
 - scrollbarWL
```
ScrollbarWithLabel scrollbarWL
```
 - channelSelectorOverlay
```
ChannelControl.ChannelSelectorOverlay channelSelectorOverlay
```
 - tiledSelectorPanel
```
Panel tiledSelectorPanel
```
 - allGrayInTilesBox
```
Checkbox allGrayInTilesBox
```
 - colorButton
```
Button colorButton
```
 - colorChooserDisplayed
```
boolean colorChooserDisplayed
```
 - cColorChooser
```
ChannelControl.ChannelColorChooser cColorChooser
```
 - nChannels
```
int nChannels
```
 - currentChannel
```
int currentChannel
```
- Class sc.fiji.i5d.gui.ChannelControl.ChannelColorCanvas extends Canvas implements Serializable
 
 serialVersionUID:
 
 3918313955836224104L
 - Serialized Fields
 - cColorChooser
```
ChannelControl.ChannelColorChooser cColorChooser
```
 - lutImage
```
Image lutImage
```
 - colorPickerImage
```
Image colorPickerImage
```
 - commonsImage
```
Image commonsImage
```
 - lutWidth
```
int lutWidth
```
 - lutHeight
```
int lutHeight
```
 - cpNHues
```
int cpNHues
```
 - cpNSats
```
int cpNSats
```
 - cpRectWidth
```
int cpRectWidth
```
 - cpRectHeight
```
int cpRectHeight
```
 - cpWidth
```
int cpWidth
```
 - cpHeight
```
int cpHeight
```
 - commonsWidth
```
int commonsWidth
```
 - commonsHeight
```
int commonsHeight
```
 - hSpacer
```
int hSpacer
```
 - vSpacer
```
int vSpacer
```
 - canvasWidth
```
int canvasWidth
```
 - canvasHeight
```
int canvasHeight
```
- Class sc.fiji.i5d.gui.ChannelControl.ChannelColorChooser extends Panel implements Serializable
 
 serialVersionUID:
 
 -2987819237979841674L
 - Serialized Fields
 - cControl
```
ChannelControl cControl
```
 - displayGrayBox
```
Checkbox displayGrayBox
```
 - editColorButton
```
Button editColorButton
```
 - editLUTButton
```
Button editLUTButton
```
 - cColorCanvas
```
ChannelControl.ChannelColorCanvas cColorCanvas
```
- Class sc.fiji.i5d.gui.ChannelControl.ChannelSelectorOverlay extends Panel implements Serializable
 
 serialVersionUID:
 
 -8138803830180530129L
 - Serialized Fields
 - cControl
```
ChannelControl cControl
```
 - allNonePanel
```
Panel allNonePanel
```
 - allButton
```
Button allButton
```
 - noneButton
```
Button noneButton
```
 - channelPane
```
ScrollPane channelPane
```
 - channelPanel
```
Panel channelPanel
```
 - channelDisplayed
```
Checkbox[] channelDisplayed
```
 - channelActive
```
Checkbox[] channelActive
```
 - channelActiveGroup
```
CheckboxGroup channelActiveGroup
```
 - nChannels
```
int nChannels
```
- Class sc.fiji.i5d.gui.Image5DCanvas extends ImageCanvas implements Serializable
 
 serialVersionUID:
 
 -8563611296852137396L
- Class sc.fiji.i5d.gui.Image5DWindow extends StackWindow implements Serializable
 
 serialVersionUID:
 
 -3196514227677416036L
 - Serialized Fields
 - channelControl
```
ChannelControl channelControl
```
 - scrollbarsWL
```
ScrollbarWithLabel[] scrollbarsWL
```
 - i5d
```
Image5D i5d
```
 - channelCanvasses
```
Vector<E> channelCanvasses
```
 - positions
```
int[] positions
```
 - nDimensions
```
int nDimensions
```
 - dimensions
```
int[] dimensions
```
 - isInitialized
```
boolean isInitialized
```
 - displayMode
```
int displayMode
```
 - displayGrayInTiles
```
boolean displayGrayInTiles
```
- Class sc.fiji.i5d.gui.ScrollbarWithLabel extends Panel implements Serializable
 
 serialVersionUID:
 
 -7934396430763922931L
 - Serialized Fields
 - bar
```
Scrollbar bar
```
 - label
```
Label label
```
 - orientation
```
int orientation
```
- Class sc.fiji.i5d.gui.TileCanvas extends Image5DCanvas implements Serializable
 
 serialVersionUID:
 
 8368953085462080966L
 - Serialized Fields
 - channel
```
int channel
```
Package sc.fiji.omevisual.gui
- Class sc.fiji.omevisual.gui.MainAppFrame extends JFrame implements Serializable
  - Serialized Fields
    - log
```
LogService log
```
    - ij
```
ImageJ ij
```
    - fxPanel
```
JFXPanel fxPanel
```
    - image
```
ImageDisplay image
```
    - md
```
OMEXMLMetadata md
```

Package sc.fiji.snt

Class sc.fiji.snt.FillManagerUI extends JDialog implements Serializable

serialVersionUID:: 1L

Serialized Fields

plugin
```
SNT plugin
```
pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
fillList
```
JList<E> fillList
```
listModel
```
DefaultListModel<E> listModel
```
gUtils
```
GuiUtils gUtils
```
maxThresholdValue
```
double maxThresholdValue
```
currentState
```
FillManagerUI.State currentState
```
manualThresholdInputField
```
JTextField manualThresholdInputField
```
maxThresholdLabel
```
JLabel maxThresholdLabel
```
currentThresholdLabel
```
JLabel currentThresholdLabel
```
cursorPositionLabel
```
JLabel cursorPositionLabel
```
fillTypeLabel
```
JLabel fillTypeLabel
```
statusText
```
JLabel statusText
```
manualThresholdApplyButton
```
JButton manualThresholdApplyButton
```
exploredThresholdApplyButton
```
JButton exploredThresholdApplyButton
```
startFill
```
JButton startFill
```
saveFill
```
JButton saveFill
```
stopFill
```
JButton stopFill
```
reloadFill
```
JButton reloadFill
```
cursorThresholdChoice
```
JRadioButton cursorThresholdChoice
```
manualThresholdChoice
```
JRadioButton manualThresholdChoice
```
exploredThresholdChoice
```
JRadioButton exploredThresholdChoice
```
exportFillsMenu
```
JPopupMenu exportFillsMenu
```
transparentCheckbox
```
JCheckBox transparentCheckbox
```
storeExtraNodesCheckbox
```
JCheckBox storeExtraNodesCheckbox
```

Class sc.fiji.snt.PathManagerUI extends JDialog implements Serializable

serialVersionUID:: 1L

Serialized Fields

tree

sc.fiji.snt.PathManagerUI.HelpfulJTree tree

plugin
```
SNT plugin
```
pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
table
```
SNTTable table
```
guiUtils
```
GuiUtils guiUtils
```
scrollPane
```
JScrollPane scrollPane
```
menuBar
```
JMenuBar menuBar
```
popup
```
JPopupMenu popup
```
swcTypeMenu
```
JMenu swcTypeMenu
```
tagsMenu
```
JMenu tagsMenu
```
swcTypeButtonGroup
```
ButtonGroup swcTypeButtonGroup
```
colorMenu
```
ColorMenu colorMenu
```
fitVolumeMenuItem
```
JMenuItem fitVolumeMenuItem
```

fittingHelper

sc.fiji.snt.PathManagerUI.FitHelper fittingHelper

searchableBar

PathManagerUISearchableBar searchableBar

Class sc.fiji.snt.SNTUI extends JDialog implements Serializable

Serialized Fields

menuBar
```
JMenuBar menuBar
```
showPathsSelected
```
JCheckBox showPathsSelected
```
showPartsNearby
```
JCheckBox showPartsNearby
```
useSnapWindow
```
JCheckBox useSnapWindow
```
onlyActiveCTposition
```
JCheckBox onlyActiveCTposition
```
snapWindowXYsizeSpinner
```
JSpinner snapWindowXYsizeSpinner
```
snapWindowZsizeSpinner
```
JSpinner snapWindowZsizeSpinner
```
nearbyFieldSpinner
```
JSpinner nearbyFieldSpinner
```
showOrHidePathList
```
JButton showOrHidePathList
```
showOrHideFillList
```
JButton showOrHideFillList
```
loadTracesMenuItem
```
JMenuItem loadTracesMenuItem
```
loadSWCMenuItem
```
JMenuItem loadSWCMenuItem
```
loadLabelsMenuItem
```
JMenuItem loadLabelsMenuItem
```
saveMenuItem
```
JMenuItem saveMenuItem
```
exportCSVMenuItem
```
JMenuItem exportCSVMenuItem
```
exportAllSWCMenuItem
```
JMenuItem exportAllSWCMenuItem
```
quitMenuItem
```
JMenuItem quitMenuItem
```
sendToTrakEM2
```
JMenuItem sendToTrakEM2
```
statusText
```
JLabel statusText
```
statusBarText
```
JLabel statusBarText
```
keepSegment
```
JButton keepSegment
```
junkSegment
```
JButton junkSegment
```
completePath
```
JButton completePath
```
rebuildCanvasButton
```
JButton rebuildCanvasButton
```
debugCheckBox
```
JCheckBox debugCheckBox
```
searchAlgoChoice
```
JComboBox<E> searchAlgoChoice
```
aStarPanel
```
JPanel aStarPanel
```
aStarCheckBox
```
JCheckBox aStarCheckBox
```
sigmaPalette
```
SigmaPalette sigmaPalette
```
commandFinder
```
SNTCommandFinder commandFinder
```
settingsArea
```
JTextArea settingsArea
```
sourcePanel
```
JPanel sourcePanel
```
secLayerPanel
```
JPanel secLayerPanel
```
secLayerActivateCheckbox
```
JCheckBox secLayerActivateCheckbox
```
secLayerBuiltinRadioButton
```
JRadioButton secLayerBuiltinRadioButton
```

secLayerExternalRadioButton

JRadioButton secLayerExternalRadioButton

secLayerGenerate
```
JButton secLayerGenerate
```

secLayerExternalImgOptionsButton

JButton secLayerExternalImgOptionsButton

secLayerExternalImgOverlayCheckbox

JCheckBox secLayerExternalImgOverlayCheckbox

secLayerExternalImgLoadFlushMenuItem

JMenuItem secLayerExternalImgLoadFlushMenuItem

activeWorker

sc.fiji.snt.SNTUI.ActiveWorker activeWorker

currentState
```
int currentState
```
plugin
```
SNT plugin
```
pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
guiUtils
```
GuiUtils guiUtils
```
pmUI
```
PathManagerUI pmUI
```
fmUI
```
FillManagerUI fmUI
```
recViewer
```
Viewer3D recViewer
```
recViewerFrame
```
Frame recViewerFrame
```
openRecViewer
```
JButton openRecViewer
```
sciViewSNT
```
SciViewSNT sciViewSNT
```
openSciView
```
JButton openSciView
```
svSyncPathManager
```
JButton svSyncPathManager
```
listener
```
sc.fiji.snt.SNTUI.GuiListener listener
```
confirmTemporarySegments
```
boolean confirmTemporarySegments
```
finishOnDoubleConfimation
```
boolean finishOnDoubleConfimation
```
discardOnDoubleCancellation
```
boolean discardOnDoubleCancellation
```
askUserConfirmation
```
boolean askUserConfirmation
```
openingSciView
```
boolean openingSciView
```

sigmaPaletteListener

SigmaPaletteListener sigmaPaletteListener

Class sc.fiji.snt.TracerCanvas extends MultiDThreePanesCanvas implements Serializable

serialVersionUID:

3620108290844138287L
- Serialized Fields
 - pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
 - just_near_slices
```
boolean just_near_slices
```
 - eitherSide
```
int eitherSide
```
 - searchArtists
```
Set<E> searchArtists
```
 - nodeSize
```
double nodeSize
```
 - transparencies
```
int[] transparencies
```
 - backBufferWidth
```
int backBufferWidth
```
 - backBufferHeight
```
int backBufferHeight
```
 - backBufferGraphics
```
Graphics2D backBufferGraphics
```
 - backBufferImage
```
Image backBufferImage
```

Package sc.fiji.snt.analysis
- Class sc.fiji.snt.analysis.SNTChart extends ChartFrame implements Serializable
  
  serialVersionUID:
  
  5245298401153759551L
- Class sc.fiji.snt.analysis.SNTTable extends DefaultGenericTable implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - hasUnsavedData
```
boolean hasUnsavedData
```
    - tableIO
```
DefaultTableIOPlugin tableIO
```
Package sc.fiji.snt.analysis.graph
- Class sc.fiji.snt.analysis.graph.AnnotationGraph extends SNTGraph<BrainAnnotation,AnnotationWeightedEdge> implements Serializable
 
 serialVersionUID:
 
 6826816297520498404L
 - Serialized Fields
 - treeCollection
```
Collection<E> treeCollection
```
 - metric
```
String metric
```
 - threshold
```
double threshold
```
 - maxOntologyDepth
```
int maxOntologyDepth
```
- Class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge extends org.jgrapht.graph.DefaultWeightedEdge implements Serializable
 
 serialVersionUID:
 
 1L
- Class sc.fiji.snt.analysis.graph.DirectedWeightedGraph extends SNTGraph<SWCPoint,SWCWeightedEdge> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - tree
```
Tree tree
```
- Class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph extends org.jgrapht.graph.AsSubgraph<SWCPoint,SWCWeightedEdge> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - graph
```
DirectedWeightedGraph graph
```
 - label
```
String label
```
- Class sc.fiji.snt.analysis.graph.SNTGraph extends org.jgrapht.graph.AbstractBaseGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> implements Serializable
 
 serialVersionUID:
 
 8458292348918037500L
 - Serialized Fields
 - vertexColorRGBMap
```
Map<K,V> vertexColorRGBMap
```
 - edgeColorRGBMap
```
Map<K,V> edgeColorRGBMap
```
 - vertexValueMap
```
Map<K,V> vertexValueMap
```
- Class sc.fiji.snt.analysis.graph.SNTPseudograph extends SNTGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> implements Serializable
 
 serialVersionUID:
 
 4375953050236896508L
- Class sc.fiji.snt.analysis.graph.SWCWeightedEdge extends org.jgrapht.graph.DefaultWeightedEdge implements Serializable
 
 serialVersionUID:
 
 1L
Package sc.fiji.snt.analysis.sholl.gui
- Class sc.fiji.snt.analysis.sholl.gui.ShollTable extends SNTTable implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - profile
```
Profile profile
```
    - stats
```
ShollStats[] stats
```
    - detailedSummary
```
boolean detailedSummary
```
    - title
```
String title
```
    - prefService
```
PrefService prefService
```
Package sc.fiji.snt.gui
- Class sc.fiji.snt.gui.ColorChooserButton extends JButton implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - current
```
Color current
```
 - listener
```
ColorChangedListener listener
```
- Class sc.fiji.snt.gui.ColorMenu extends JMenu implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - _colorPanes
```
Map<K,V> _colorPanes
```
 - _selectedColorPane
```
sc.fiji.snt.gui.ColorMenu.ColorPane _selectedColorPane
```
 - _activeBorder
```
Border _activeBorder
```
 - _selectedBorder
```
Border _selectedBorder
```
 - _unselectedBorder
```
Border _unselectedBorder
```
- Class sc.fiji.snt.gui.EnhancedGenericDialog extends GenericDialogPlus implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - labelOfHelpActionButton
```
String labelOfHelpActionButton
```
 Deprecated.
 - helpActionButtonListener
```
ActionListener helpActionButtonListener
```
 Deprecated.
 - helpActionMouseListener
```
MouseAdapter helpActionMouseListener
```
 Deprecated.
- Class sc.fiji.snt.gui.EnhancedWaitForUserDialog extends WaitForUserDialog implements Serializable
 
 serialVersionUID:
 
 1L
- Class sc.fiji.snt.gui.GuiUtils.JTextFieldFile extends sc.fiji.snt.gui.GuiUtils.TextFieldWithPlaceholder implements Serializable
 
 serialVersionUID:
 
 6943445407475634685L
 - Serialized Fields
 - file
```
File file
```
 - tooltipPrefix
```
String tooltipPrefix
```
 - defaultColor
```
Color defaultColor
```
- Class sc.fiji.snt.gui.PathManagerUISearchableBar extends SNTSearchableBar implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - pmui
```
PathManagerUI pmui
```
 - guiUtils
```
GuiUtils guiUtils
```
 - subFilteringEnabled
```
boolean subFilteringEnabled
```
- Class sc.fiji.snt.gui.ShollAnalysisDialog extends JDialog implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - x_start
```
double x_start
```
 Deprecated.
 - y_start
```
double y_start
```
 Deprecated.
 - z_start
```
double z_start
```
 Deprecated.
 - pathsGroup
```
ButtonGroup pathsGroup
```
 Deprecated.
 - useAllPathsCheckbox
```
JRadioButton useAllPathsCheckbox
```
 Deprecated.
 - useSelectedPathsCheckbox
```
JRadioButton useSelectedPathsCheckbox
```
 Deprecated.
 - swcTypesButton
```
JButton swcTypesButton
```
 Deprecated.
 - swcTypesMenu
```
JPopupMenu swcTypesMenu
```
 Deprecated.
 - filteredTypes
```
ArrayList<E> filteredTypes
```
 Deprecated.
 - filteredTypesWarningLabel
```
JLabel filteredTypesWarningLabel
```
 Deprecated.
 - makeShollImageButton
```
JButton makeShollImageButton
```
 Deprecated.
 - exportProfileButton
```
JButton exportProfileButton
```
 Deprecated.
 - drawShollGraphButton
```
JButton drawShollGraphButton
```
 Deprecated.
 - analyzeButton
```
JButton analyzeButton
```
 Deprecated.
 - axesGroup
```
ButtonGroup axesGroup
```
 Deprecated.
 - normalAxes
```
JRadioButton normalAxes
```
 Deprecated.
 - semiLogAxes
```
JRadioButton semiLogAxes
```
 Deprecated.
 - logLogAxes
```
JRadioButton logLogAxes
```
 Deprecated.
 - normalizationGroup
```
ButtonGroup normalizationGroup
```
 Deprecated.
 - noNormalization
```
JRadioButton noNormalization
```
 Deprecated.
 - normalizationForSphereVolume
```
JRadioButton normalizationForSphereVolume
```
 Deprecated.
 - exportPath
```
String exportPath
```
 Deprecated.
 - margin
```
int margin
```
 Deprecated.
 - graphFrame
```
sc.fiji.snt.gui.ShollAnalysisDialog.GraphFrame graphFrame
```
 Deprecated.
 - numberOfSelectedPaths
```
int numberOfSelectedPaths
```
 Deprecated.
 - numberOfAllPaths
```
int numberOfAllPaths
```
 Deprecated.
 - sampleSeparation
```
double sampleSeparation
```
 Deprecated.
 - shollPointsAllPaths
```
ArrayList<E> shollPointsAllPaths
```
 Deprecated.
 - shollPointsSelectedPaths
```
ArrayList<E> shollPointsSelectedPaths
```
 Deprecated.
 - shollpafm
```
PathAndFillManager shollpafm
```
 Deprecated.
 - resultsPanel
```
sc.fiji.snt.gui.ShollAnalysisDialog.ResultsPanel resultsPanel
```
 Deprecated.
 - gUtils
```
GuiUtils gUtils
```
 Deprecated.
 - plugin
```
SNT plugin
```
 Deprecated.
- Class sc.fiji.snt.gui.SNTSearchableBar extends com.jidesoft.swing.SearchableBar implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - _extraButtons
```
List<E> _extraButtons
```
 - containsCheckboxes
```
boolean containsCheckboxes
```
 - buttonHeight
```
int buttonHeight
```
 - iconHeight
```
float iconHeight
```
 - buttonCount
```
int buttonCount
```
 - statusLabelPlaceholder
```
String statusLabelPlaceholder
```
 - objectDescription
```
String objectDescription
```
 - guiUtils
```
GuiUtils guiUtils
```
 - findAndReplaceMenuItem
```
JMenuItem findAndReplaceMenuItem
```
- Class sc.fiji.snt.gui.SWCImportOptionsDialog extends JDialog implements Serializable
 - Serialized Fields
 - succeeded
```
boolean succeeded
```
 - replaceExistingPathsCheckbox
```
JCheckBox replaceExistingPathsCheckbox
```
 - ignoreCalibrationCheckbox
```
JCheckBox ignoreCalibrationCheckbox
```
 - applyOffsetCheckbox
```
JCheckBox applyOffsetCheckbox
```
 - applyScaleCheckbox
```
JCheckBox applyScaleCheckbox
```
 - offsetDefault
```
String offsetDefault
```
 - scaleDefault
```
String scaleDefault
```
 - xOffsetTextField
```
JTextField xOffsetTextField
```
 - yOffsetTextField
```
JTextField yOffsetTextField
```
 - zOffsetTextField
```
JTextField zOffsetTextField
```
 - xScaleTextField
```
JTextField xScaleTextField
```
 - yScaleTextField
```
JTextField yScaleTextField
```
 - zScaleTextField
```
JTextField zScaleTextField
```
 - okButton
```
JButton okButton
```
 - cancelButton
```
JButton cancelButton
```
 - restoreToDefaultsButton
```
JButton restoreToDefaultsButton
```
Package sc.fiji.snt.hyperpanes
- Class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas extends ImageCanvas implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - owner
```
PaneOwner owner
```
    - plane
```
int plane
```
    - current_x
```
double current_x
```
    - current_y
```
double current_y
```
    - current_z
```
double current_z
```
    - draw_crosshairs
```
boolean draw_crosshairs
```
    - cursorText
```
String cursorText
```
    - canvasText
```
String canvasText
```
    - annotationsColor
```
Color annotationsColor
```
    - waveInteractionsToIJ
```
boolean waveInteractionsToIJ
```
    - waitingForRoiDrawing
```
boolean waitingForRoiDrawing
```
    - cursorLocked
```
boolean cursorLocked
```
Package sc.fiji.snt.viewer
- Class sc.fiji.snt.viewer.Viewer3D.ManagerPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - guiUtils
```
GuiUtils guiUtils
```
    - table
```
SNTTable table
```
    - debugCheckBox
```
JCheckBoxMenuItem debugCheckBox
```
    - searchableBar
```
SNTSearchableBar searchableBar
```
    - progressBar
```
sc.fiji.snt.viewer.Viewer3D.ManagerPanel.ProgressBar progressBar
```
    - cmdFinder
```
SNTCommandFinder cmdFinder
```
Package sc.fiji.snt.viewer.geditor
- Class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent extends SNTGraphComponent implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - layout
```
com.mxgraph.layout.mxGraphLayout layout
```
 - forceConstant
```
double forceConstant
```
 - minDistance
```
double minDistance
```
 - maxDistance
```
double maxDistance
```
 - initialTemp
```
double initialTemp
```
 - maxIterations
```
double maxIterations
```
 - radius
```
double radius
```
- Class sc.fiji.snt.viewer.geditor.GraphEditor extends JPanel implements Serializable
 
 serialVersionUID:
 
 -6561623072112577140L
 - Serialized Fields
 - context
```
Context context
```
 - prefService
```
PrefService prefService
```
 - graphComponent
```
com.mxgraph.swing.mxGraphComponent graphComponent
```
 - graphOutline
```
com.mxgraph.swing.mxGraphOutline graphOutline
```
 - libraryPane
```
JTabbedPane libraryPane
```
 - undoManager
```
com.mxgraph.util.mxUndoManager undoManager
```
 - appTitle
```
String appTitle
```
 - statusBar
```
JLabel statusBar
```
 - currentFile
```
File currentFile
```
 - rubberband
```
com.mxgraph.swing.handler.mxRubberband rubberband
```
 - keyboardHandler
```
com.mxgraph.swing.handler.mxKeyboardHandler keyboardHandler
```
 - editorConsole
```
sc.fiji.snt.viewer.geditor.EditorConsole editorConsole
```
 - legendPanel
```
JPanel legendPanel
```
 - mainPanel
```
JSplitPane mainPanel
```
 - bottomPanel
```
JSplitPane bottomPanel
```
 - toolbar
```
sc.fiji.snt.viewer.geditor.EditorToolBar toolbar
```
 - animateLayoutChange
```
boolean animateLayoutChange
```
 - annotationMetricJCombo
```
JComboBox<E> annotationMetricJCombo
```
 - annotationThresholdField
```
JFormattedTextField annotationThresholdField
```
 - annotationDepthField
```
JFormattedTextField annotationDepthField
```
 - modified
```
boolean modified
```
 Flag indicating whether the current graph has been modified
 - undoHandler
```
com.mxgraph.util.mxEventSource.mxIEventListener undoHandler
```
 - changeTracker
```
com.mxgraph.util.mxEventSource.mxIEventListener changeTracker
```
- Class sc.fiji.snt.viewer.geditor.SNTGraphComponent extends com.mxgraph.swing.mxGraphComponent implements Serializable
 
 serialVersionUID:
 
 -341155071963647372L
 - Serialized Fields
 - cmdService
```
CommandService cmdService
```
 - adapter
```
SNTGraphAdapter<V,E extends org.jgrapht.graph.DefaultWeightedEdge> adapter
```
 - saveDir
```
File saveDir
```
 - spaceDown
```
boolean spaceDown
```
 - editor
```
GraphEditor editor
```
- Class sc.fiji.snt.viewer.geditor.SNTPseudographComponent extends SNTGraphComponent implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - layout
```
com.mxgraph.layout.mxGraphLayout layout
```
- Class sc.fiji.snt.viewer.geditor.TreeGraphComponent extends SNTGraphComponent implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - layout
```
com.mxgraph.layout.mxCompactTreeLayout layout
```
Package sc.fiji.timelapse
- Class sc.fiji.timelapse.DummyCanvas extends ImageCanvas implements Serializable
- Class sc.fiji.timelapse.PolygonRoiPublic extends PolygonRoi implements Serializable
  - Serialized Fields
    - specifiedByUser
```
boolean specifiedByUser
```
    - normalStrokeColor
```
Color normalStrokeColor
```
    - specifiedStrokeColor
```
Color specifiedStrokeColor
```
Package script.imglib.analysis
- Class script.imglib.analysis.BarChart extends JFrame implements Serializable
 
 serialVersionUID:
 
 7347559630675867104L
 - Serialized Fields
 - chart
```
JFreeChart chart
```
- Class script.imglib.analysis.DoGPeaks extends ArrayList<float[]> implements Serializable
 
 serialVersionUID:
 
 7614417748092214062L
 - Serialized Fields
 - peaks
```
List<E> peaks
```
- Class script.imglib.analysis.Histogram extends TreeMap<Double,Integer> implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - img
```
Image<T extends Type<T>> img
```
 - min
```
double min
```
 - max
```
double max
```
 - increment
```
double increment
```
- Class script.imglib.analysis.PickPeaks extends ArrayList<float[]> implements Serializable
 
 serialVersionUID:
 
 5392390381529251353L
Package selection
- Class selection.ExtendedPointMatch extends PointMatch implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - radius1L
```
double radius1L
```
    - radius1W
```
double radius1W
```
    - radius2L
```
double radius2L
```
    - radius2W
```
double radius2W
```
Package siox
- Class siox.ControlJPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1037100741242680537L
  - Serialized Fields
    - segJPanel
```
JPanel segJPanel
```
    - drbJPanel
```
JPanel drbJPanel
```
    - resetJPanel
```
JPanel resetJPanel
```
    - fgOrBgJLabel
```
JLabel fgOrBgJLabel
```
    - segmentJButton
```
JButton segmentJButton
```
    - fgJRadioButton
```
JRadioButton fgJRadioButton
```
    - bgJRadioButton
```
JRadioButton bgJRadioButton
```
    - smoothness
```
JSlider smoothness
```
    - multipart
```
JCheckBox multipart
```
    - smoothJLabel
```
JLabel smoothJLabel
```
    - addJRadioButton
```
JRadioButton addJRadioButton
```
    - subJRadioButton
```
JRadioButton subJRadioButton
```
    - refineJButton
```
JButton refineJButton
```
    - addThreshold
```
JSlider addThreshold
```
    - subThreshold
```
JSlider subThreshold
```
    - resetJButton
```
JButton resetJButton
```
    - createMaskJButton
```
JButton createMaskJButton
```
    - saveSegmentatorJButton
```
JButton saveSegmentatorJButton
```
    - status
```
int status
```
      One of the status constants, denotes current processing step.
- Class siox.SegmentationGUI extends ImageWindow implements Serializable
  
  serialVersionUID:
  
  -326288432966353440L
  - Serialized Fields
    - confMatrix
```
ij.process.FloatProcessor confMatrix
```
      Confidence matrix
    - siox
```
SioxSegmentator siox
```
    - lastButton
```
JRadioButton lastButton
```
    - foregroundRoi
```
Roi foregroundRoi
```
    - backgroundRoi
```
Roi backgroundRoi
```
    - roiOverlay
```
RoiOverlay roiOverlay
```
    - addRoi
```
Roi addRoi
```
    - subRoi
```
Roi subRoi
```
    - resultOverlay
```
ImageOverlay resultOverlay
```
    - controlPanel
```
ControlJPanel controlPanel
```
    - ip
```
ij.process.ImageProcessor ip
```
    - transparency050
```
Composite transparency050
```
    - transparency075
```
Composite transparency075
```
    - transparency100
```
Composite transparency100
```
- Class siox.SegmentationInfo extends Object implements Serializable
  
  serialVersionUID:
  
  -87458916146804009L
  - Serialized Fields
    - bgSignature
```
float[][] bgSignature
```
      background color signature
    - fgSignature
```
float[][] fgSignature
```
      foreground color signature
    - smoothness
```
int smoothness
```
      number of smoothing steps in the post processing
    - sizeFactorToKeep
```
double sizeFactorToKeep
```
      Segmentation retains the largest connected foreground component plus any component with size at least sizeOfLargestComponent/sizeFactorToKeep
Package spim.fiji.plugin.thinout
- Class spim.fiji.plugin.thinout.Histogram extends ApplicationFrame implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - min
```
double min
```
    - max
```
double max
```
Package spim.fiji.plugin.util
- Class spim.fiji.plugin.util.MyMultiLineLabel extends Canvas implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - lines
```
String[] lines
```
    - num_lines
```
int num_lines
```
    - margin_width
```
int margin_width
```
    - margin_height
```
int margin_height
```
    - line_height
```
int line_height
```
    - line_ascent
```
int line_ascent
```
    - line_widths
```
int[] line_widths
```
    - min_width
```
int min_width
```
    - max_width
```
int max_width
```
    - gd
```
GenericDialog gd
```
    - panel
```
Panel panel
```

Package spim.fiji.spimdata.explorer

Class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel extends JPanel implements Serializable

serialVersionUID:: -3767947754096099774L

Serialized Fields

table
```
JTable table
```

tableModel

ViewSetupTableModel<AS extends AbstractSpimData<?>> tableModel

listeners
```
ArrayList<E> listeners
```

data

AbstractSpimData<S extends AbstractSequenceDescription<?,?,?>> data

explorer

ViewSetupExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> explorer

xml
```
String xml
```

io

XmlIoAbstractSpimData<S extends AbstractSequenceDescription<?,?,?>,T extends AbstractSpimData<S>> io

isMac
```
boolean isMac
```
colorMode
```
boolean colorMode
```
selectedRows
```
HashSet<E> selectedRows
```

firstSelectedVD

BasicViewDescription<V extends BasicViewSetup> firstSelectedVD

Class spim.fiji.spimdata.explorer.ViewSetupTableModel extends AbstractTableModel implements Serializable

serialVersionUID:: -6526338840427674269L

Serialized Fields

elements
```
ArrayList<E> elements
```

panel

ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel

columnNames
```
ArrayList<E> columnNames
```
registrationColumn
```
int registrationColumn
```
interestPointsColumn
```
int interestPointsColumn
```
viewRegistrations
```
ViewRegistrations viewRegistrations
```
viewInterestPoints
```
ViewInterestPoints viewInterestPoints
```

Package spim.fiji.spimdata.explorer.interestpoint
- Class spim.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 -3767947754096099774L
 - Serialized Fields
 - viewSetupExplorer
```
ViewSetupExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> viewSetupExplorer
```
 - table
```
JTable table
```
 - tableModel
```
InterestPointTableModel tableModel
```
 - label
```
JLabel label
```
 - delete
```
ArrayList<E> delete
```
- Class spim.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel.MyRenderer extends DefaultTableCellRenderer implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - backgroundColor
```
Color backgroundColor
```
- Class spim.fiji.spimdata.explorer.interestpoint.InterestPointTableModel extends AbstractTableModel implements Serializable
 
 serialVersionUID:
 
 -1263388435427674269L
 - Serialized Fields
 - viewInterestPoints
```
ViewInterestPoints viewInterestPoints
```
 - columnNames
```
ArrayList<E> columnNames
```
 - currentVD
```
BasicViewDescription<V extends BasicViewSetup> currentVD
```
 - panel
```
InterestPointExplorerPanel panel
```
 - selectedRow
```
int selectedRow
```
 - selectedCol
```
int selectedCol
```
 - interestPointSources
```
ArrayList<E> interestPointSources
```
 - interestPointOverlay
```
InterestPointOverlay interestPointOverlay
```
 - points
```
Collection<E> points
```
Package spim.fiji.spimdata.explorer.popup
- Class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.BakeManualTransformationPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 4627408819269954486L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.BDVPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
 - bdv
```
BigDataViewer bdv
```
- Class spim.fiji.spimdata.explorer.popup.BoundingBoxPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.DetectInterestPointsPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.DisplayViewPopup extends JMenu implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.FusionPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
 - ipe
```
InterestPointExplorer<AS extends SpimData2,X extends XmlIoAbstractSpimData<?,AS>> ipe
```
- Class spim.fiji.spimdata.explorer.popup.LabelPopUp extends JLabel implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
- Class spim.fiji.spimdata.explorer.popup.MaxProjectPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.RegistrationExplorerPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
 - re
```
RegistrationExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> re
```
- Class spim.fiji.spimdata.explorer.popup.RemoveDetectionsPopup extends JMenu implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup extends JMenu implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.ReorientSamplePopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.ResavePopup extends JMenu implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.Separator extends JSeparator implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
- Class spim.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
- Class spim.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup extends JMenuItem implements Serializable
 
 serialVersionUID:
 
 5234649267634013390L
 - Serialized Fields
 - panel
```
ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> panel
```
Package spim.fiji.spimdata.explorer.registration
- Class spim.fiji.spimdata.explorer.registration.RegistrationExplorerPanel extends JPanel implements Serializable
 
 serialVersionUID:
 
 -3767947754096099774L
 - Serialized Fields
 - explorer
```
RegistrationExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>> explorer
```
 - table
```
JTable table
```
 - tableModel
```
RegistrationTableModel tableModel
```
 - label
```
JLabel label
```
 - cache
```
ArrayList<E> cache
```
- Class spim.fiji.spimdata.explorer.registration.RegistrationTableModel extends AbstractTableModel implements Serializable
 
 serialVersionUID:
 
 -1263388435427674269L
 - Serialized Fields
 - viewRegistrations
```
ViewRegistrations viewRegistrations
```
 - columnNames
```
ArrayList<E> columnNames
```
 - panel
```
RegistrationExplorerPanel panel
```
 - currentVD
```
BasicViewDescription<V extends BasicViewSetup> currentVD
```
Package spim.fiji.spimdata.interestpoints
- Class spim.fiji.spimdata.interestpoints.InterestPoint extends Point implements Serializable
  
  serialVersionUID:
  
  5615112297702152070L
  - Serialized Fields
    - id
```
int id
```
- Class spim.fiji.spimdata.interestpoints.InterestPointValue extends InterestPoint implements Serializable
  
  serialVersionUID:
  
  -4538307380458133556L
  - Serialized Fields
    - intensity
```
double intensity
```
Package spim.process.interestpointregistration
- Class spim.process.interestpointregistration.Detection extends Point implements Serializable
  
  serialVersionUID:
  
  -1512879446587557778L
  - Serialized Fields
    - id
```
int id
```
    - weight
```
double weight
```
    - useW
```
boolean useW
```
    - distance
```
double distance
```
    - isUsed
```
boolean isUsed
```
Package spim.process.interestpointregistration.registrationstatistics
- Class spim.process.interestpointregistration.registrationstatistics.GraphFrame extends JFrame implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - chart
```
JFreeChart chart
```
 - chartPanel
```
ChartPanel chartPanel
```
 - mouseListener
```
MouseListenerTimelapse mouseListener
```
 - mainPanel
```
JPanel mainPanel
```
- Class spim.process.interestpointregistration.registrationstatistics.SelectTimepointEntry extends AbstractAction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - data
```
ArrayList<E> data
```
 - chartPanel
```
ChartPanel chartPanel
```
Package spim.vecmath
- Class spim.vecmath.AxisAngle4d extends Object implements Serializable
  
  serialVersionUID:
  
  3644296204459140589L
  - Serialized Fields
    - x
```
double x
```
      The x coordinate.
    - y
```
double y
```
      The y coordinate.
    - z
```
double z
```
      The z coordinate.
    - angle
```
double angle
```
      The angle of rotation in radians.
- Class spim.vecmath.AxisAngle4f extends Object implements Serializable
  
  serialVersionUID:
  
  -163246355858070601L
  - Serialized Fields
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
    - angle
```
float angle
```
      The angle of rotation in radians.
- Class spim.vecmath.Color3f extends Tuple3f implements Serializable
  
  serialVersionUID:
  
  -1861792981817493659L
- Class spim.vecmath.Matrix3d extends Object implements Serializable
  
  serialVersionUID:
  
  6837536777072402710L
  - Serialized Fields
    - m00
```
double m00
```
      The first matrix element in the first row.
    - m01
```
double m01
```
      The second matrix element in the first row.
    - m02
```
double m02
```
      The third matrix element in the first row.
    - m10
```
double m10
```
      The first matrix element in the second row.
    - m11
```
double m11
```
      The second matrix element in the second row.
    - m12
```
double m12
```
      The third matrix element in the second row.
    - m20
```
double m20
```
      The first matrix element in the third row.
    - m21
```
double m21
```
      The second matrix element in the third row.
    - m22
```
double m22
```
      The third matrix element in the third row.
- Class spim.vecmath.Matrix3f extends Object implements Serializable
  
  serialVersionUID:
  
  329697160112089834L
  - Serialized Fields
    - m00
```
float m00
```
      The first matrix element in the first row.
    - m01
```
float m01
```
      The second matrix element in the first row.
    - m02
```
float m02
```
      The third matrix element in the first row.
    - m10
```
float m10
```
      The first matrix element in the second row.
    - m11
```
float m11
```
      The second matrix element in the second row.
    - m12
```
float m12
```
      The third matrix element in the second row.
    - m20
```
float m20
```
      The first matrix element in the third row.
    - m21
```
float m21
```
      The second matrix element in the third row.
    - m22
```
float m22
```
      The third matrix element in the third row.
- Class spim.vecmath.Matrix4d extends Object implements Serializable
  
  serialVersionUID:
  
  8223903484171633710L
  - Serialized Fields
    - m00
```
double m00
```
      The first element of the first row.
    - m01
```
double m01
```
      The second element of the first row.
    - m02
```
double m02
```
      The third element of the first row.
    - m03
```
double m03
```
      The fourth element of the first row.
    - m10
```
double m10
```
      The first element of the second row.
    - m11
```
double m11
```
      The second element of the second row.
    - m12
```
double m12
```
      The third element of the second row.
    - m13
```
double m13
```
      The fourth element of the second row.
    - m20
```
double m20
```
      The first element of the third row.
    - m21
```
double m21
```
      The second element of the third row.
    - m22
```
double m22
```
      The third element of the third row.
    - m23
```
double m23
```
      The fourth element of the third row.
    - m30
```
double m30
```
      The first element of the fourth row.
    - m31
```
double m31
```
      The second element of the fourth row.
    - m32
```
double m32
```
      The third element of the fourth row.
    - m33
```
double m33
```
      The fourth element of the fourth row.
- Class spim.vecmath.Matrix4f extends Object implements Serializable
  
  serialVersionUID:
  
  -8405036035410109353L
  - Serialized Fields
    - m00
```
float m00
```
      The first element of the first row.
    - m01
```
float m01
```
      The second element of the first row.
    - m02
```
float m02
```
      The third element of the first row.
    - m03
```
float m03
```
      The fourth element of the first row.
    - m10
```
float m10
```
      The first element of the second row.
    - m11
```
float m11
```
      The second element of the second row.
    - m12
```
float m12
```
      The third element of the second row.
    - m13
```
float m13
```
      The fourth element of the second row.
    - m20
```
float m20
```
      The first element of the third row.
    - m21
```
float m21
```
      The second element of the third row.
    - m22
```
float m22
```
      The third element of the third row.
    - m23
```
float m23
```
      The fourth element of the third row.
    - m30
```
float m30
```
      The first element of the fourth row.
    - m31
```
float m31
```
      The second element of the fourth row.
    - m32
```
float m32
```
      The third element of the fourth row.
    - m33
```
float m33
```
      The fourth element of the fourth row.
- Class spim.vecmath.Point3d extends Tuple3d implements Serializable
  
  serialVersionUID:
  
  5718062286069042927L
- Class spim.vecmath.Point3f extends Tuple3f implements Serializable
  
  serialVersionUID:
  
  -8689337816398030143L
- Class spim.vecmath.Point3i extends Tuple3i implements Serializable
  
  serialVersionUID:
  
  6149289077348153921L
- Class spim.vecmath.Point4d extends Tuple4d implements Serializable
  
  serialVersionUID:
  
  1733471895962736949L
- Class spim.vecmath.Point4f extends Tuple4f implements Serializable
  
  serialVersionUID:
  
  4643134103185764459L
- Class spim.vecmath.Quat4d extends Tuple4d implements Serializable
  
  serialVersionUID:
  
  7577479888820201099L
- Class spim.vecmath.Quat4f extends Tuple4f implements Serializable
  
  serialVersionUID:
  
  2675933778405442383L
- Class spim.vecmath.SingularMatrixException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -6776952045336842169L
- Class spim.vecmath.Tuple3d extends Object implements Serializable
  
  serialVersionUID:
  
  5542096614926168415L
  - Serialized Fields
    - x
```
double x
```
      The x coordinate.
    - y
```
double y
```
      The y coordinate.
    - z
```
double z
```
      The z coordinate.
- Class spim.vecmath.Tuple3f extends Object implements Serializable
  
  serialVersionUID:
  
  5019834619484343712L
  - Serialized Fields
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
- Class spim.vecmath.Tuple3i extends Object implements Serializable
  
  serialVersionUID:
  
  -732740491767276200L
  - Serialized Fields
    - x
```
int x
```
      The x coordinate.
    - y
```
int y
```
      The y coordinate.
    - z
```
int z
```
      The z coordinate.
- Class spim.vecmath.Tuple4d extends Object implements Serializable
  
  serialVersionUID:
  
  -4748953690425311052L
  - Serialized Fields
    - x
```
double x
```
      The x coordinate.
    - y
```
double y
```
      The y coordinate.
    - z
```
double z
```
      The z coordinate.
    - w
```
double w
```
      The w coordinate.
- Class spim.vecmath.Tuple4f extends Object implements Serializable
  
  serialVersionUID:
  
  7068460319248845763L
  - Serialized Fields
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
    - w
```
float w
```
      The w coordinate.
- Class spim.vecmath.Vector3d extends Tuple3d implements Serializable
  
  serialVersionUID:
  
  3761969948420550442L
- Class spim.vecmath.Vector3f extends Tuple3f implements Serializable
  
  serialVersionUID:
  
  -7031930069184524614L
- Class spim.vecmath.Vector4d extends Tuple4d implements Serializable
  
  serialVersionUID:
  
  3938123424117448700L
- Class spim.vecmath.Vector4f extends Tuple4f implements Serializable
  
  serialVersionUID:
  
  8749319902347760659L
Package spimopener
- Class spimopener.DoubleSlider extends Panel implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - minTF
```
TextField minTF
```
 - maxTF
```
TextField maxTF
```
 - incTF
```
TextField incTF
```
 - slider
```
spimopener.DoubleSlider.DoubleSliderCanvas slider
```
- Class spimopener.OpenerGenericDialog extends GenericDialogPlus implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - listener
```
ActionListener listener
```
 - doubleSliders
```
List<E> doubleSliders
```
 - cIdx
```
int cIdx
```
 - okButton
```
Button okButton
```

Package stacks

Class stacks.ThreePaneContainer extends StackWindow implements Serializable

Serialized Fields

original_xy_canvas
```
ThreePanesCanvas original_xy_canvas
```
xy
```
ij.ImagePlus xy
```
xz
```
ij.ImagePlus xz
```
zy
```
ij.ImagePlus zy
```
xy_canvas
```
ThreePanesCanvas xy_canvas
```
xz_canvas
```
ThreePanesCanvas xz_canvas
```
zy_canvas
```
ThreePanesCanvas zy_canvas
```

Class stacks.ThreePaneCropCanvas extends ThreePanesCanvas implements Serializable

Serialized Fields

crop_min_offscreen_x
```
int crop_min_offscreen_x
```
crop_max_offscreen_x
```
int crop_max_offscreen_x
```
crop_min_offscreen_y
```
int crop_min_offscreen_y
```
crop_max_offscreen_y
```
int crop_max_offscreen_y
```
offscreen_width
```
int offscreen_width
```
offscreen_height
```
int offscreen_height
```
dragging
```
int dragging
```
x_pressed_at
```
int x_pressed_at
```
y_pressed_at
```
int y_pressed_at
```
offset_x_in_handle
```
int offset_x_in_handle
```
offset_y_in_handle
```
int offset_y_in_handle
```
nw
```
stacks.CropHandleRectangle nw
```
ne
```
stacks.CropHandleRectangle ne
```
sw
```
stacks.CropHandleRectangle sw
```
se
```
stacks.CropHandleRectangle se
```
backBufferWidth
```
int backBufferWidth
```
backBufferHeight
```
int backBufferHeight
```
backBufferGraphics
```
Graphics backBufferGraphics
```
backBufferImage
```
Image backBufferImage
```

Class stacks.ThreePanesCanvas extends ImageCanvas implements Serializable
- Serialized Fields
  - owner
```
PaneOwner owner
```
  - plane
```
int plane
```
  - current_x
```
double current_x
```
  - current_y
```
double current_y
```
  - current_z
```
double current_z
```
  - draw_crosshairs
```
boolean draw_crosshairs
```

Package stitching.model
- Class stitching.model.NoninvertibleModelException extends Exception implements Serializable
- Class stitching.model.NotEnoughDataPointsException extends Exception implements Serializable
Package trainableSegmentation
- Class trainableSegmentation.ReusableDenseInstance extends DenseInstance implements Serializable
  
  serialVersionUID:
  
  -2322621365960366756L
Package util
- Class util.BatchOpener.ImageLoaderException extends Exception implements Serializable
- Class util.BatchOpener.NoSuchChannelException extends Exception implements Serializable
- Class util.Histogram_2D.HistogramOptionsDialog extends Dialog implements Serializable
- Class util.ModelessQuestions extends Dialog implements Serializable
 - Serialized Fields
 - components
```
ArrayList<E> components
```
 - imagePlus
```
ij.ImagePlus imagePlus
```
 - checkboxGroups
```
Hashtable<K,V> checkboxGroups
```
 - completingButtons
```
ArrayList<E> completingButtons
```
 - buttonPressed
```
int buttonPressed
```

Package vib

Class vib.Points_Dialog extends Dialog implements Serializable

Serialized Fields

panel
```
vib.Points_Dialog.PointsPanel panel
```
popup
```
PopupMenu popup
```
cal
```
ij.measure.Calibration cal
```
imp
```
ij.ImagePlus imp
```
points
```
PointList points
```
current
```
BenesNamedPoint current
```

Class vib.SegmentationViewerCanvas extends ImageCanvas implements Serializable

Serialized Fields

mode
```
int mode
```
alpha
```
int alpha
```
labels
```
ij.ImagePlus labels
```
w
```
int w
```
h
```
int h
```
d
```
int d
```
label_colors
```
Color[] label_colors
```
contours
```
Vector<E>[] contours
```
colors
```
Vector<E>[] colors
```
indices
```
Vector<E>[] indices
```
debug
```
boolean debug
```
backBufferWidth
```
int backBufferWidth
```
backBufferHeight
```
int backBufferHeight
```
backBufferGraphics
```
Graphics backBufferGraphics
```
backBufferImage
```
Image backBufferImage
```

Class vib.ShowHistogram extends ImageWindow implements Serializable

Serialized Fields

histogram
```
double[] histogram
```
histMin
```
double histMin
```
binSize
```
double binSize
```
frame
```
Rectangle frame
```
list
```
Button list
```
save
```
Button save
```
copy
```
Button copy
```
log
```
Button log
```
value
```
Label value
```
count
```
Label count
```
decimalPlaces
```
int decimalPlaces
```
digits
```
int digits
```
newMinCount
```
int newMinCount
```
newMaxCount
```
int newMaxCount
```
plotScale
```
int plotScale
```
logScale
```
boolean logScale
```
yMax
```
int yMax
```

Package vib.app
- Class vib.app.FileGroup extends ArrayList<File> implements Serializable
 - Serialized Fields
 - name
```
String name
```
Package vib.app.gui
- Class vib.app.gui.FileGroupDialog extends Panel implements Serializable
  - Serialized Fields
    - files
```
FileGroup files
```
    - showWholePath
```
boolean showWholePath
```
    - list
```
List list
```
    - nameTF
```
TextField nameTF
```
    - add
```
Button add
```
    - delete
```
Button delete
```
    - template
```
Button template
```
    - wholePath
```
Checkbox wholePath
```
    - showTemplateButton
```
boolean showTemplateButton
```

Package vib.segment

Class vib.segment.CustomCanvas extends SegmentationViewerCanvas implements Serializable
- Serialized Fields
 - listener
```
Vector<E> listener
```
Class vib.segment.CustomStackWindow extends StackWindow implements Serializable
- Serialized Fields
  - savedRois
```
Roi[] savedRois
```
  - oldSlice
```
int oldSlice
```
  - roisLocked
```
boolean roisLocked
```
  - al
```
ActionListener al
```
  - sidebar
```
Sidebar sidebar
```
  - cc
```
CustomCanvas cc
```
  - ok
```
Button ok
```
Class vib.segment.ImageButton extends Canvas implements Serializable
- Serialized Fields
 - tracker
```
MediaTracker tracker
```
 - images
```
Image[] images
```
 - borders
```
Border[] borders
```
 - generatedDisabled
```
boolean generatedDisabled
```
 - mousedown
```
boolean mousedown
```
 - buttonState
```
int buttonState
```
 - command
```
String command
```
 - borderColor
```
Color borderColor
```
 - actionListeners
```
Vector<E> actionListeners
```
Class vib.segment.InfoPanel extends Panel implements Serializable
- Serialized Fields
  - lPosX
```
Label lPosX
```
  - lPosY
```
Label lPosY
```
  - lPosZ
```
Label lPosZ
```
  - lIndexX
```
Label lIndexX
```
  - lIndexY
```
Label lIndexY
```
  - lIndexZ
```
Label lIndexZ
```
  - lMaterialName
```
Label lMaterialName
```
  - lVoxelValueNum
```
Label lVoxelValueNum
```
  - font
```
Font font
```

Class vib.segment.MaterialList extends ScrollPane implements Serializable

Serialized Fields

popup
```
PopupMenu popup
```
labels
```
ij.ImagePlus labels
```
params
```
AmiraParameters params
```
cc
```
CustomCanvas cc
```
font
```
Font font
```
lineHeight
```
int lineHeight
```
lineWidth
```
int lineWidth
```
list
```
vib.segment.MaterialList.List list
```
locked
```
boolean[] locked
```
remove
```
MenuItem remove
```
add
```
MenuItem add
```
rename
```
MenuItem rename
```
color
```
MenuItem color
```
lock
```
CheckboxMenuItem lock
```

Class vib.segment.Sidebar extends Panel implements Serializable

Serialized Fields

cc
```
CustomCanvas cc
```
font
```
Font font
```
constr
```
GridBagConstraints constr
```
lZoomLevel
```
Label lZoomLevel
```
bZoomPlus
```
ImageButton bZoomPlus
```
bZoomMinus
```
ImageButton bZoomMinus
```
bPlus
```
ImageButton bPlus
```
bMinus
```
ImageButton bMinus
```
bInterpolate
```
ImageButton bInterpolate
```
bThreshold
```
ImageButton bThreshold
```
bOpen
```
ImageButton bOpen
```
bClose
```
ImageButton bClose
```
check3d
```
Checkbox check3d
```
labelImagesChoice
```
Choice labelImagesChoice
```
labelImages
```
Vector<E> labelImages
```
al
```
ActionListener al
```
materials
```
MaterialList materials
```
defaultMaterials
```
Vector<E> defaultMaterials
```
currentLabelsAreNew
```
boolean currentLabelsAreNew
```

Package view5d

Class view5d.AlternateViewer extends Frame implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - cloned
```
My3DData cloned
```
  - mycomponent
```
Component mycomponent
```
  - applet
```
Container applet
```

Class view5d.ImageCanvas extends Canvas implements Serializable

serialVersionUID:: 1L

Serialized Fields

dadd
```
int dadd
```
xprev
```
int xprev
```
yprev
```
int yprev
```
ROIs
```
int ROIs
```
ROIe
```
int ROIe
```
LineROIStarted
```
boolean LineROIStarted
```
LROIs
```
int LROIs
```
LROIe
```
int LROIe
```
ROIMoveStarted
```
boolean ROIMoveStarted
```
ROIMoveStartX
```
int ROIMoveStartX
```
ROIMoveStartY
```
int ROIMoveStartY
```
ROIMoveDX
```
int ROIMoveDX
```
ROIMoveDY
```
int ROIMoveDY
```
tmpROIPolygons
```
Polygon tmpROIPolygons
```
ImgDragStarted
```
boolean ImgDragStarted
```
ximgdrag
```
int ximgdrag
```
yimgdrag
```
int yimgdrag
```
imgw
```
int imgw
```
imgh
```
int imgh
```
scale
```
double scale
```
LineData
```
double[] LineData
```
AxisData
```
double[] AxisData
```
XAxisTitle
```
String XAxisTitle
```
YAxisTitle
```
String YAxisTitle
```
AspectFromView
```
boolean AspectFromView
```
AspectLocked
```
CheckboxMenuItem AspectLocked
```
focus
```
boolean focus
```
DispPlot
```
boolean DispPlot
```
curimage
```
Image curimage
```
applet
```
Container applet
```
myPanel
```
ImgPanel myPanel
```
otherCanvas1
```
ImageCanvas otherCanvas1
```
otherCanvas2
```
ImageCanvas otherCanvas2
```
my3ddata
```
My3DData my3ddata
```
PlanesXs
```
Vector<E> PlanesXs
```
PlanesYs
```
Vector<E> PlanesYs
```
PlanesXe
```
Vector<E> PlanesXe
```
PlanesYe
```
Vector<E> PlanesYe
```
hastoinit
```
boolean hastoinit
```
DimNr
```
int DimNr
```
mytitle
```
String mytitle
```
label
```
PositionLabel label
```
MyPopupMenu
```
PopupMenu MyPopupMenu
```
PositionValue
```
double PositionValue
```
DataOffset
```
double DataOffset
```
MaxPos
```
int MaxPos
```

Class view5d.ImageErr extends TextArea implements Serializable

serialVersionUID:

1L

Class view5d.ImgPanel extends Panel implements Serializable

serialVersionUID:: 1L

Serialized Fields

applet
```
Container applet
```
DataPanel
```
ImgPanel DataPanel
```
data3d
```
My3DData data3d
```
c1
```
ImageCanvas c1
```
c2
```
ImageCanvas c2
```
c3
```
ImageCanvas c3
```
label
```
PositionLabel label
```
ROIstarted
```
boolean ROIstarted
```
DraggedMarker
```
view5d.APoint DraggedMarker
```
SavedMarker
```
view5d.APoint SavedMarker
```
MyMenu
```
MenuBar MyMenu
```
ScrollbarPresent
```
boolean ScrollbarPresent
```
OldOffset
```
double[] OldOffset
```

Class view5d.PixelDisplay extends Panel implements Serializable

serialVersionUID:: 1L

Serialized Fields

c1
```
ImageCanvas c1
```
c2
```
ImageCanvas c2
```
c3
```
ImageCanvas c3
```
data3d
```
My3DData data3d
```
imgw
```
int imgw
```
imgh
```
int imgh
```
lxold
```
int lxold
```
lyold
```
int lyold
```
PointNr
```
int PointNr
```
pval
```
double pval
```
didinit
```
boolean didinit
```
PlotMode
```
int PlotMode
```
myInfo
```
view5d.PlotInfo myInfo
```
normalize
```
boolean normalize
```
logmode
```
boolean logmode
```
maxdispl
```
double maxdispl
```
mindispl
```
double mindispl
```
TextToDisplay
```
String TextToDisplay
```
MyPopupMenu
```
PopupMenu MyPopupMenu
```
ColorMenu
```
Menu ColorMenu
```

Class view5d.PositionLabel extends Panel implements Serializable

serialVersionUID:: 1L

Serialized Fields

c1
```
ImageCanvas c1
```
c2
```
ImageCanvas c2
```
c3
```
ImageCanvas c3
```
data3d
```
My3DData data3d
```
l1
```
Label l1
```
l2
```
Label l2
```
l3
```
Label l3
```
l4
```
Label l4
```
l5
```
Label l5
```
l6
```
Label l6
```
PixDisplay
```
PixelDisplay PixDisplay
```
MyText
```
TextArea MyText
```
nf
```
NumberFormat nf
```
nf2
```
NumberFormat nf2
```
TimeScrollbar
```
Scrollbar TimeScrollbar
```
px
```
int px
```
py
```
int py
```
pz
```
int pz
```
pt
```
int pt
```
lnr
```
int lnr
```
lpos
```
int lpos
```
MyPopupMenu
```
PopupMenu MyPopupMenu
```
DispIntScaleOffset
```
CheckboxMenuItem DispIntScaleOffset
```
DispPosSizePix
```
CheckboxMenuItem DispPosSizePix
```
DispPosWorld
```
CheckboxMenuItem DispPosWorld
```
DispROIInfo
```
CheckboxMenuItem DispROIInfo
```
DispCoordScales
```
CheckboxMenuItem DispCoordScales
```
DispThreshColor
```
CheckboxMenuItem DispThreshColor
```
DispListNrPos
```
CheckboxMenuItem DispListNrPos
```
DispMarkerInfo
```
CheckboxMenuItem DispMarkerInfo
```

Class view5d.View5D extends Applet implements Serializable

serialVersionUID:: 2L

Serialized Fields

SizeX
```
int SizeX
```
SizeY
```
int SizeY
```
SizeZ
```
int SizeZ
```
Elements
```
int Elements
```
Times
```
int Times
```
defaultColor0
```
int defaultColor0
```
redEl
```
int redEl
```
greenEl
```
int greenEl
```
blueEl
```
int blueEl
```
data3d
```
My3DData data3d
```
myLabel
```
TextArea myLabel
```
mypan
```
ImgPanel mypan
```
aviewer
```
AlternateViewer aviewer
```
panels
```
Vector<E> panels
```
filename
```
String filename
```

Class view5d.View5D_ extends ij.plugin.frame.PlugInFrame implements Serializable

serialVersionUID:: 2L

Serialized Fields

previousId
```
int previousId
```
imp
```
ij.ImagePlus imp
```
ip
```
ij.process.ImageProcessor ip
```
data3d
```
My3DData data3d
```
myLabel
```
TextArea myLabel
```
IJMenu
```
MenuBar IJMenu
```
panels
```
Vector<E> panels
```
DimensionChoices
```
String[] DimensionChoices
```
AppendChoices
```
String[] AppendChoices
```
AspectFromData
```
boolean AspectFromData
```
SizeX
```
int SizeX
```
SizeY
```
int SizeY
```
SizeZ
```
int SizeZ
```
Elements
```
int Elements
```
Times
```
int Times
```
DimensionOrder
```
int DimensionOrder
```
AppendTo
```
int AppendTo
```

Package volumeCalculator

Class volumeCalculator.VolumesPanel extends Panel implements Serializable

Serialized Fields

constraints
```
GridBagConstraints constraints
```
colorChooser
```
ColorChooser colorChooser
```
volumes
```
Volumes volumes
```
Where all the values for the different colored volumes are kept.
checkboxGroup
```
CheckboxGroup checkboxGroup
```
volumeLabels
```
List<E> volumeLabels
```

analyzedGraph

volumeCalculator.AnalyzedGraph analyzedGraph

universe
```
Image3DUniverse universe
```
addColorVolumeButton
```
Button addColorVolumeButton
```
boundingBoxCheckbox
```
Checkbox boundingBoxCheckbox
```
keyNavigationOnlyCheckbox
```
Checkbox keyNavigationOnlyCheckbox
```
panel1
```
Panel panel1
```
panel2
```
Panel panel2
```
scrollPane1
```
ScrollPane scrollPane1
```
statusLabel
```
Label statusLabel
```
volumeUnitsLabel
```
Label volumeUnitsLabel
```
volumesPanel
```
Panel volumesPanel
```

Serialized Form

Package <Unnamed>

Class BorderPanel extends Panel implements Serializable

Serialized Fields

label

Class Color_Inspector_3D.Menu extends JMenuBar implements Serializable

Serialized Fields

stringColor

stringText

stringAxes

stringRotation

stringResetManip

stringFitImage

stringEnglish

stringManual

stringError1

stringOpen

stringSaveVisualisation

stringSaveModified

stringDuplicateVisualisation

stringDuplicateModified

stringQuit

stringGradient

stringComic

stringStart

stringphoto

stringCG

stringPalette

stringWebColors

stringColorCube1

stringColorCube2

stringSeg1

stringSeg2

stringSeg3

stringSeg4

stringSeg5

stringSeg6

Class DisplayChangeEvent extends EventObject implements Serializable

Serialized Fields

type

value

Class HybridDateFormat extends DateFormat implements Serializable

Serialization Methods

readObject

Serialized Fields

formatData

defaultCenturyStart

pattern

serialVersionOnStream

Class IntField extends TextField implements Serializable

Serialized Fields

value

minValue

maxValue

actionCommand

Class IntSlider extends Panel implements Serializable

Serialized Fields

bar

field

value

minValue

maxValue

actionCommand

Class Manual_Tracking extends ij.plugin.frame.PlugInFrame implements Serializable

Serialized Fields

calxy

calz

calt

cent

dotsize

linewidth

fontsize

col

i

j

k

l

m

n

txt