Sync_Measure_3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Frame
      - ij.plugin.frame.PlugInFrame
        
        Sync_Windows
        
        Sync_Measure_3D

All Implemented Interfaces:

DisplayChangeListener, ij.ImageListener, ij.plugin.PlugIn, ActionListener, FocusListener, ItemListener, MouseListener, MouseMotionListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible
```
public class Sync_Measure_3D
extends Sync_Windows
```
This PlugIn synchronizes the cursor and z-slice in all selected windows, and performs measurements on 3D ROIs in all selected windows. With the PlugIn one can measure - the chromatic shift of a microscope by measuring the intensity gravity centers of multispectral beads in all color channels simultaneously - central positions, volumes and total intensities of objects in an image stack - the 3D distance of several signals (e.g. genes) from a common reference point (e.g. the intensity gravity center of the nucleus). - relative 3D distances of signals - ... Installation instructions: Place Sync_Win.jar into the ImageJ plugins directory or a subdirectory and restart ImageJ. Sync Windows and Sync Measure 3D can be found under the menu entry Analyze>Tools. Usage instructions: - Load the data, each color channel as a separate 8-bit grayscale stack. - Run Sync_Measure_3D (Analyze>Tools>Sync Measure 3D). - Synchronize the windows, in which you want to measure by selecting them in the window list. - Click "Start Measurements". - Click on "Projection" to obtain a combined maximum intensity projection of all selected images (stacks). This projection is not used for measurements, but is synchronized with the other images and might be a convenient reference. - Choose a threshold for each image. - Measure gravity center, Volume, Intensity and distance to preceding stacks: o Draw a ROI around the particle you want to measure. If the particles in different channels are at different positions, turn "Synchronize Cursor" off for that. o If necessary (when other particles are inside the ROI in different z-slices), Select first and last slice to include this particle and exclude the other ones. o Double-click (left mousebutton) into the ROI to perform a measurement. + The X, Y and Z values are the coordinates of the intensity gravity centers of the measured objects. + The Volume and Intensity values are the volumes and the total intensities of the measured objects. + The Dist 1, Dist 2, ... values (for 2 or more image stacks) are the 3D distances of the intensity gravity center of the object in the current stack to the intensity gravity center of the object in the first, second, ... stack in the list. + If the scale of the image is not set, the results are displayed in "pixels". 3D-distances are meaningless in this case, if the distance between slices differs from the pixelsize. If the image scale is set, the results are displayed in the selected unit. + Intensity values are given in gray values or the selected units in case that the image has been density calibrated. If the image is density calibrated, the centers of mass are calculated with the calibrated values, but the threshold is still a raw value (0-255 for 8-bit images). o To calculate mean values and standard deviations, click on "Stop Measurements". + For the x- y- and z- coordinates the differences to the coordinates of image stack #1 are calculated ( (value for this stack) minus (value for stack #1) ) and their mean and standard deviation values are displayed. This helps in calculating the chromatic shift to stack #1. + For the Dist 1, Dist 2, ... values, simply the mean and the standard deviation are calculated.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class java.awt.Frame
  Frame.AccessibleAWTFrame
- Nested classes/interfaces inherited from class java.awt.Window
  Window.AccessibleAWTWindow, Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

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

Fields inherited from class Sync_Windows
bSyncAll, bUnsyncAll, cChannel, cCoords, cCursor, cFrame, cScaling, cSlice, ijInstance, oldX, oldY, panel, VERSIONSTRING, vListMap, vwins, wList, x, y

Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description

Sync_Measure_3D()

Sync_Measure_3D(String s)

Constructors
Constructor and Description
`Sync_Measure_3D()`
`Sync_Measure_3D(String s)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`actionPerformed(ActionEvent e)` Implementation of ActionListener interface.
`protected Panel`	`buildCommonControls()` Builds the Panel with buttons and textfields for first and last slice and for projection.
`protected ScrollPane`	`buildMeasureControl()` Builds the Panel with Scrollbars to adjust the threshold for each image and with buttons to select the first and the last slice.
`void`	`calcFinal()` Calculates the shift from the measured intensity gravity centers.
`protected Panel`	`controlPanel()` Build window list display and button controls.
`void`	`imageClosed(ij.ImagePlus imp)` Implementation of ImageListener interface: update window list, if image is opened or closed
`void`	`imageOpened(ij.ImagePlus imp)` Implementation of ImageListener interface: update window list, if image is opened or closed
`protected void`	`measure(ij.ImagePlus image, int x, int y)` This method does the actual measuring work.
`void`	`mousePressed(MouseEvent e)` Propagate mouse pressed events to all synchronized windows.
`void`	`run(String args)` Show the frame, making it accessible to users.
`protected void`	`setControlsEnabled(boolean enable)` greys off and on the control elements for adding and removing windows
`protected void`	`showAbout()`
`void`	`startMeasurements()`
`void`	`stopMeasurements()` Removes contact to everything that is not further needed.
`protected int`	`stringToInt(String s)`
`protected void`	`updateScrollbars()` Sets the threshold values in the images from the scrollbar positions.
`protected void`	`updateThreshold(int iWin)` Sets the threshold value in the image window iWin from the scrollbar position.
`void`	`windowActivated(WindowEvent e)`
`void`	`windowClosing(WindowEvent e)` Override parent windowClosing method to clean up synchronized resources on exit.

Methods inherited from class Sync_Windows
boundingRect, buildControlPanel, buildWindowList, displayChanged, getImageFromVector, getImageTitleFromVector, getIndexOfImage, getMatchingCoords, imageUpdated, itemStateChanged, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mouseReleased, updateWindowList

Methods inherited from class ij.plugin.frame.PlugInFrame
close, focusGained, focusLost, windowClosed, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.awt.Frame
addNotify, getAccessibleContext, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, paramString, remove, removeNotify, setBackground, setCursor, setExtendedState, setIconImage, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusDownCycle, update, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer
getFont, postEvent

- Field Detail
  - DEFAULT_FIRST_SLICE
```
protected int DEFAULT_FIRST_SLICE
```
  - DEFAULT_LAST_SLICE
```
protected int DEFAULT_LAST_SLICE
```
  - measuring
```
protected boolean measuring
```
  - bMeasure
```
protected Button bMeasure
```
  - measurePanel
```
protected Panel measurePanel
```
  - vScrollThresh
```
protected Vector vScrollThresh
```
  - I_THRESH_SLIDER
```
protected final String I_THRESH_SLIDER
```
    See Also:
    
    Constant Field Values
  - vFirstButton
```
protected Vector vFirstButton
```
  - I_FIRST_SLICE_BUTTON
```
protected final String I_FIRST_SLICE_BUTTON
```
    See Also:
    
    Constant Field Values
  - vFirstInt
```
protected Vector vFirstInt
```
  - iFirstSlice
```
protected int[] iFirstSlice
```
  - I_FIRST_SLICE_BOX
```
protected final String I_FIRST_SLICE_BOX
```
    See Also:
    
    Constant Field Values
  - vLastButton
```
protected Vector vLastButton
```
  - I_LAST_SLICE_BUTTON
```
protected final String I_LAST_SLICE_BUTTON
```
    See Also:
    
    Constant Field Values
  - vLastInt
```
protected Vector vLastInt
```
  - iLastSlice
```
protected int[] iLastSlice
```
  - I_LAST_SLICE_BOX
```
protected final String I_LAST_SLICE_BOX
```
    See Also:
    
    Constant Field Values
  - bFirstSlice
```
protected Button bFirstSlice
```
  - intFirstSlice
```
protected IntField intFirstSlice
```
  - COMMON_FIRST_SLICE_BOX
```
protected final String COMMON_FIRST_SLICE_BOX
```
    See Also:
    
    Constant Field Values
  - bLastSlice
```
protected Button bLastSlice
```
  - intLastSlice
```
protected IntField intLastSlice
```
  - COMMON_LAST_SLICE_BOX
```
protected final String COMMON_LAST_SLICE_BOX
```
    See Also:
    
    Constant Field Values
  - bProjection
```
protected Button bProjection
```
  - hasProjection
```
protected boolean hasProjection
```
  - projection
```
protected ij.ImagePlus projection
```
  - resultsTable
```
protected Sync_Measure_3D.M3DRTab resultsTable
```
  - resultsWindow
```
protected Sync_Measure_3D.M3DRWin resultsWindow
```
  - nWindows
```
protected int nWindows
```
  - mOptions
```
protected int mOptions
```
  - nQuantities
```
protected int nQuantities
```
  - nRelQuantities
```
protected int nRelQuantities
```
- Constructor Detail
  - Sync_Measure_3D
```
public Sync_Measure_3D()
```
  - Sync_Measure_3D
```
public Sync_Measure_3D(String s)
```
- Method Detail
  - run
```
public void run(String args)
```
    Description copied from class: Sync_Windows
    
    Show the frame, making it accessible to users.
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
    
    Overrides:
    
    run in class Sync_Windows
  - controlPanel
```
protected Panel controlPanel()
```
    Description copied from class: Sync_Windows
    
    Build window list display and button controls. Create Hashtable that connects list entries to window IDs.
    
    Overrides:
    
    controlPanel in class Sync_Windows
  - actionPerformed
```
public void actionPerformed(ActionEvent e)
```
    Implementation of ActionListener interface.
    
    Specified by:
    
    actionPerformed in interface ActionListener
    
    Overrides:
    
    actionPerformed in class Sync_Windows
  - startMeasurements
```
public void startMeasurements()
```
  - stopMeasurements
```
public void stopMeasurements()
```
    Removes contact to everything that is not further needed.
  - windowClosing
```
public void windowClosing(WindowEvent e)
```
    Description copied from class: Sync_Windows
    
    Override parent windowClosing method to clean up synchronized resources on exit.
    
    Specified by:
    
    windowClosing in interface WindowListener
    
    Overrides:
    
    windowClosing in class Sync_Windows
  - windowActivated
```
public void windowActivated(WindowEvent e)
```
    Specified by:
    
    windowActivated in interface WindowListener
    
    Overrides:
    
    windowActivated in class ij.plugin.frame.PlugInFrame
  - mousePressed
```
public void mousePressed(MouseEvent e)
```
    Description copied from class: Sync_Windows
    
    Propagate mouse pressed events to all synchronized windows.
    
    Specified by:
    
    mousePressed in interface MouseListener
    
    Overrides:
    
    mousePressed in class Sync_Windows
  - imageOpened
```
public void imageOpened(ij.ImagePlus imp)
```
    Implementation of ImageListener interface: update window list, if image is opened or closed
    
    Specified by:
    
    imageOpened in interface ij.ImageListener
    
    Overrides:
    
    imageOpened in class Sync_Windows
  - imageClosed
```
public void imageClosed(ij.ImagePlus imp)
```
    Implementation of ImageListener interface: update window list, if image is opened or closed
    
    Specified by:
    
    imageClosed in interface ij.ImageListener
    
    Overrides:
    
    imageClosed in class Sync_Windows
  - buildMeasureControl
```
protected ScrollPane buildMeasureControl()
```
    Builds the Panel with Scrollbars to adjust the threshold for each image and with buttons to select the first and the last slice. The Panel is embedded into a ScrollPane, which has a maximum height of 380 pixels. Up to 5 images can be controlled without scrolling.
  - buildCommonControls
```
protected Panel buildCommonControls()
```
    Builds the Panel with buttons and textfields for first and last slice and for projection.
  - setControlsEnabled
```
protected void setControlsEnabled(boolean enable)
```
    greys off and on the control elements for adding and removing windows
  - updateScrollbars
```
protected void updateScrollbars()
```
    Sets the threshold values in the images from the scrollbar positions.
  - updateThreshold
```
protected void updateThreshold(int iWin)
```
    Sets the threshold value in the image window iWin from the scrollbar position.
  - measure
```
protected void measure(ij.ImagePlus image,
                       int x,
                       int y)
```
    This method does the actual measuring work. Spatial units are pixels (by default) or the selected units in case that the scale of the image has been set. Intensity values are given in gray values or the selected units in case that the image has been density calibrated. If the image is density calibrated, the centers of mass are calculated with the calibrated values. The threshold, however, is always a raw value (0-255 for 8-bit images). This behaviour is consistent with the behaviour of the "measure" function of ImageJ. The parameters image, x, y are not used here, but are usefull for extending Sync_Measure_3D.
  - calcFinal
```
public void calcFinal()
```
    Calculates the shift from the measured intensity gravity centers. The calculated values are the shift of a position in each image to the position in the first image and the standard deviation. The order is (position in image) Minus (position in first image).
  - stringToInt
```
protected int stringToInt(String s)
```
  - showAbout
```
protected void showAbout()
```
    Overrides:
    
    showAbout in class Sync_Windows

Class Sync_Measure_3D

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Frame

Nested classes/interfaces inherited from class java.awt.Window

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class Sync_Windows

Fields inherited from class java.awt.Frame

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class Sync_Windows

Methods inherited from class ij.plugin.frame.PlugInFrame

Methods inherited from class java.awt.Frame

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface java.awt.MenuContainer

Field Detail

DEFAULT_FIRST_SLICE

DEFAULT_LAST_SLICE

measuring

bMeasure

measurePanel

vScrollThresh

I_THRESH_SLIDER

vFirstButton

I_FIRST_SLICE_BUTTON

vFirstInt

iFirstSlice

I_FIRST_SLICE_BOX

vLastButton

I_LAST_SLICE_BUTTON

vLastInt

iLastSlice

I_LAST_SLICE_BOX

bFirstSlice

intFirstSlice

COMMON_FIRST_SLICE_BOX

bLastSlice

intLastSlice

COMMON_LAST_SLICE_BOX

bProjection

hasProjection

projection

resultsTable

resultsWindow

nWindows

mOptions

nQuantities

nRelQuantities

Constructor Detail

Sync_Measure_3D

Sync_Measure_3D

Method Detail

run

controlPanel

actionPerformed

startMeasurements

stopMeasurements

windowClosing

windowActivated

mousePressed

imageOpened

imageClosed

buildMeasureControl

buildCommonControls

setControlsEnabled

updateScrollbars

updateThreshold

measure

calcFinal

stringToInt

showAbout