Constant Field Values

Contents

• fiji.plugin.*

fiji.plugin.*

fiji.plugin.trackmate.ModelChangeEvent

Modifier and Type	Constant Field	Value
public static final int	FEATURES_COMPUTED	9
public static final int	FLAG_EDGE_ADDED	4
public static final int	FLAG_EDGE_MODIFIED	6
public static final int	FLAG_EDGE_REMOVED	5
public static final int	FLAG_SPOT_ADDED	0
public static final int	FLAG_SPOT_FRAME_CHANGED	3
public static final int	FLAG_SPOT_MODIFIED	2
public static final int	FLAG_SPOT_REMOVED	1
public static final int	MODEL_MODIFIED	8
public static final int	SPOTS_COMPUTED	4
public static final int	SPOTS_FILTERED	5
public static final int	TRACKS_COMPUTED	6
public static final int	TRACKS_VISIBILITY_CHANGED	7

fiji.plugin.trackmate.Spot

Modifier and Type	Constant Field	Value
public static final String	FRAME	"FRAME"
public static final String	POSITION_T	"POSITION_T"
public static final String	POSITION_X	"POSITION_X"
public static final String	POSITION_Y	"POSITION_Y"
public static final String	POSITION_Z	"POSITION_Z"
public static final String	QUALITY	"QUALITY"
public static final String	RADIUS	"RADIUS"

fiji.plugin.trackmate.SpotCollection

Modifier and Type	Constant Field	Value
public static final String	VISIBILITY	"VISIBILITY"

fiji.plugin.trackmate.TrackMate

Modifier and Type	Constant Field	Value
public static final String	PLUGIN_NAME_STR	"TrackMate"

fiji.plugin.trackmate.action.CaptureOverlayAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>If the current displayer is the HyperstackDisplayer, this action <br>will capture the TrackMate overlay with current display settings. <br>That is: a new RGB stack will be created (careful with large data) where <br>each frame contains a RGB snapshot of the TrackMate display. <p>It can take long since we pause between each frame to ensure the whole <br>overlay is redrawn. The current zoom is taken into account. <br>Also, make sure nothing is moved over the image while capturing. </html>"
public static final String	KEY	"CAPTURE_OVERLAY"
public static final String	NAME	"Capture overlay"

fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	FEATURE	"DISTANCE_TO_ROI"
public static final String	NAME	"Distance to ROI"

fiji.plugin.trackmate.action.CTCExporterAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Export the current TrackMate session to the Cell-Tracking-Challenge file format.<p>See the <a url=\"http://celltrackingchallenge.net/\">challenge webpage</a> for details: http://celltrackingchallenge.net</html>"
public static final String	KEY	"CTC_EXPORTER"
public static final String	NAME	"Export to CTC format"

fiji.plugin.trackmate.action.ExportAllSpotsStatsAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Export the statistics of all spots to a table. The numerical features of all visible spots are exported, regardless of whether they are in a track or not.</html>"
public static final String	KEY	"EXPORT_ALL_SPOTS_STATS"
public static final String	NAME	"Export all spots statistics"

fiji.plugin.trackmate.action.ExportStatsTablesAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Compute and export all statistics to 3 tables. Statistics are separated in features computed for: <ol> \t<li> spots in visible tracks; \t<li> edges between those spots; \t<li> visible tracks. </ol> Note that spots and edges that are not in visible tracks won\'t be displayed in the tables.</html>"
public static final String	KEY	"EXPORT_STATS"
public static final String	NAME	"Export statistics to tables"

fiji.plugin.trackmate.action.ExportTracksToXML

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Export the tracks in the current model content to a XML file in a simple format. <p> The file will have one element per track, and each track contains several spot elements. These spots are sorted by frame number, and have 4 numerical attributes: the frame number this spot is in, and its X, Y, Z position in physical units as specified in the image properties. <p>As such, this format <u>cannot</u> handle track merging and splitting properly, and is suited only for non-branching tracks.</html>"
public static final String	KEY	"EXPORT_TRACKS_TO_XML_SIMPLE"
public static final String	NAME	"Export tracks to XML file"

fiji.plugin.trackmate.action.ExtractTrackStackAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html> Generate a stack of images taken from the track that joins two selected spots. <p> There must be exactly 1 or 2 spots selected for this action to work. If only one spot is selected, then the stack is extracted from the track it belongs to, from the first spot in time to the last in time. If there are two spots selected, they must belong to a track that connects them. A path is then found that joins them and the stack is extracted from this path.<p> A stack of images will be generated from the spots that join them. A GUI allows specifying the size of the extract, in units of the largest spot in the track, and whether to capture a 2D or 3D stack over time. All channels are captured. </html>"
public static final String	KEY	"EXTRACT_TRACK_STACK"
public static final String	NAME	"Extract track stack"

fiji.plugin.trackmate.action.ISBIChallengeExporter

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Export the current model content to a XML file following the ISBI 2012 single particle tracking challenge format, as specified on <a href=\'http://bioimageanalysis.org/track/\'></a>. <p> Only tracks are exported. If there is no track, this action does nothing. </html>"
public static final String	KEY	"EXPORT_TO_ISBI_CHALLENGE_FORMAT"
public static final String	NAME	"Export to ISBI challenge file format"

fiji.plugin.trackmate.action.LabelImgExporter

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This action creates a label image from the tracking results. <p> A new 32-bit image is generated, of same dimension and size that of the input image. The label image has one channel, with black background (0 value) everywhere, except where there are spots. Each spot is painted with a uniform integer value, configurable to be the spot ID, the ID of the track it belongs to, or a simple index, unique to the frame or to the movie. <p> Only visible spots are painted. </html>"
public static final String	KEY	"EXPORT_LABEL_IMG"
public static final String	NAME	"Export label image"

fiji.plugin.trackmate.action.MergeFileAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Merge the current model with the data from another <br>file, specified by the user. This is useful <i>e.g.</i> <br>if two operators have been annotating the same datasets <br>and want to merge their work in a single file.<p>Only the spots belonging to visible tracks are imported <br>from the target file, which makes this action non-entirely <br>symmetrical. Numerical features are re-calculated using <br>the current settings. There is no check that the imported <br>data was generated on the raw source.</html>"
public static final String	KEY	"MERGE_OTHER_FILE"
public static final String	NAME	"Merge a TrackMate file"

fiji.plugin.trackmate.action.MotilityLabExporter

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Display the visible tracks in a spreadsheet that can be copy-pasted directly into the <a url=\"http://www.motilitylab.net/import/data-import.php\"> MotilityLab website</a> for further track analysis."
public static final String	KEY	"MOTILITYLAB_EXPORTER"
public static final String	NAME	"Export to MotilityLab spreadsheet"

fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Plot the number of spots in each frame as a function <br>of time. Only the filtered spots are taken into account. </html>"
public static final String	KEY	"PLOT_NSPOTS_VS_TIME"
public static final String	NAME	"Plot N spots vs time"

fiji.plugin.trackmate.action.RecomputeFeatureAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Calling this action causes the model to recompute all the features values for all spots, edges and tracks. All the feature analyzers discovered when running this action are added and computed. </html>"
public static final String	KEY	"RECOMPUTE_FEATURES"
public static final String	NAME	"Recompute all features"

fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Reset the time feature of all spots: it is set to the frame number times the frame interval. </html>"
public static final String	NAME	"Reset spot time"

fiji.plugin.trackmate.action.TrimNotVisibleAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This action trims the tracking data by removing anything that is not marked as visible. <p>The spots that do not belong to a visible track will be removed. The tracks that are not marked as visible will be removed as well. <p>This action is irreversible. It helps limiting the memory and disk space of tracking data that has been properly curated.</html>"
public static final String	KEY	"TRIM_NOT_VISIBLE"
public static final String	NAME	"Trim non-visible data"

fiji.plugin.trackmate.action.autonaming.AutoNamingAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Rename individual spots based on auto-naming rules. All spot names are changed. There is no undo.</html>"

fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory

Modifier and Type	Constant Field	Value
public static final String	KEY	"AUTO_NAMING"
public static final String	NAME	"Spot auto-naming"

fiji.plugin.trackmate.action.closegaps.CloseGapsAction

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This action proposes several methods to close gaps in tracks.<p>Gaps are part of tracks where spots are missing in one or several consecutive frames. The listed methods can introduce new spots in such gaps, depending on possibly the other spots in tracks and/or the image data.<p>They are useful to fix missed detection when a uninterrupted list of position is required for track analysis. For instance in FRAP experiments, where you need to measure signal intensity changing during time, even if the spot is not visible.</html>"
public static final String	KEY	"CLOSE_GAPS"
public static final String	NAME	"Close gaps by introducing new spots"

fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This method allows to close gaps in tracks by executing a detection in the vicinity of linearly interpolated position over a gap.<p>The same detector and detection settings than for the initial detection step are used. The search volume is built by taking a box of twice the interpolated radius of the source and target spots at the gap.<p>This method is best if there is a single spot near a missed detection that could be recognized by the detection process executed in a smaller region. It is well suited to be used with detectors that use a normalized threshold, like the Hessian detector.</html>"
public static final String	NAME	"Close gaps by detection"

fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This action allows to close gaps in tracks by intercalating new spots in gaps which position is interpolated from the positions of the true spots at the gap beginning and end. The image data is not used to adjust the position of spots.</html>"
public static final String	NAME	"Close gaps by interpolating positions"

fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This action launches a GUI for the sub-localization of spots using gaussian peak fitting. <p>The fit process will update the spot position and their radius, using the results from the gaussian fit. Of course it works best when the peaks in the image ressemble gaussian functions. The fitting process uses the spots information (position and radius) as initial values for the fit.<p>It works for both 2D and 3D images. In 3D it accounts for non-isotropic calibration (and possible PSF deformation in the Z direction) thanks to an elliptic gaussian function, with axes constrained to be along X, Y and Z. In 2D we use an isotropic gaussian.</html>"
public static final String	KEY	"GAUSS_FIT"
public static final String	NAME	"Refine spot position with gaussian fitting"

fiji.plugin.trackmate.detection.DetectorKeys

Modifier and Type	Constant Field	Value
public static final boolean	DEFAULT_DO_MEDIAN_FILTERING	false
public static final boolean	DEFAULT_DO_SUBPIXEL_LOCALIZATION	true
public static final int	DEFAULT_DOWNSAMPLE_FACTOR	4
public static final boolean	DEFAULT_NORMALIZE	false
public static final double	DEFAULT_RADIUS	5.0
public static final double	DEFAULT_RADIUS_Z	8.0
public static final int	DEFAULT_TARGET_CHANNEL	1
public static final double	DEFAULT_THRESHOLD	0.0
public static final String	KEY_DO_MEDIAN_FILTERING	"DO_MEDIAN_FILTERING"
public static final String	KEY_DO_SUBPIXEL_LOCALIZATION	"DO_SUBPIXEL_LOCALIZATION"
public static final String	KEY_DOWNSAMPLE_FACTOR	"DOWNSAMPLE_FACTOR"
public static final String	KEY_NORMALIZE	"NORMALIZE"
public static final String	KEY_RADIUS	"RADIUS"
public static final String	KEY_RADIUS_Z	"RADIUS_Z"
public static final String	KEY_TARGET_CHANNEL	"TARGET_CHANNEL"
public static final String	KEY_THRESHOLD	"THRESHOLD"
public static final String	XML_ATTRIBUTE_DETECTOR_NAME	"DETECTOR_NAME"

fiji.plugin.trackmate.detection.DogDetector<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	BASE_ERROR_MESSAGE	"DogDetector: "

fiji.plugin.trackmate.detection.DogDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	THIS_DETECTOR_KEY	"DOG_DETECTOR"
public static final String	THIS_INFO_TEXT	"<html>This detector is based on an approximation of the LoG operator <br> by differences of Gaussian (DoG). Computations are made in direct space. <br>It is the quickest for small spot sizes (< ~5 pixels). <p> Spots found too close are suppressed. This detector can do sub-pixel <br>localization of spots using a quadratic fitting scheme. It is based on <br>the scale-space framework made by Stephan Preibisch for ImgLib. </html>"
public static final String	THIS_NAME	"DoG detector"

fiji.plugin.trackmate.detection.HessianDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"HESSIAN_DETECTOR"
public static final String	INFO_TEXT	"<html>This detector is based on computing the determinant of the <br>Hessian matrix of the image to detector bright blobs. <p>It can be configured with a different spots size in XY and Z. <br>It can also return a normalized quality value, scaled from 0 <br>to 1 for the spots of each time-point.<p>As discussed in Mikolajczyk et al.(2005), this detector has <br>a better edge response elimination than the LoG detector and is <br>suitable for detect spots in images with many strong edges.</html>"
public static final String	NAME	"Hessian detector"

fiji.plugin.trackmate.detection.LabelImageDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"LABEL_IMAGE_DETECTOR"
public static final String	INFO_TEXT	"<html>This detector creates spots by importing regions from a label image.<p>A label image is an image where the pixel values are integers. Each object in a label image is represented by a single common pixel value (the label) that is unique to the object.<p>This detector reads such an image and create spots from each object. In 2D the contour of a label is imported. In 3D, spherical spots of the same volume that the label are created.<p>The spot quality stores the object area or volume in pixels.</html>"
public static final String	NAME	"Label image detector"

fiji.plugin.trackmate.detection.LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"LOG_DETECTOR"
public static final String	INFO_TEXT	"<html>This detector applies a LoG (Laplacian of Gaussian) filter <br>to the image, with a sigma suited to the blob estimated size. <br>Calculations are made in the Fourier space. The maxima in the <br>filtered image are searched for, and maxima too close from each <br>other are suppressed. A quadratic fitting scheme allows to do <br>sub-pixel localization. </html>"
public static final String	NAME	"LoG detector"

fiji.plugin.trackmate.detection.ManualDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"MANUAL_DETECTOR"
public static final String	INFO_TEXT	"<html>Selecting this will skip the automatic detection phase, and jump directly <br>to manual segmentation. A default spot size will be asked for. </html>"
public static final String	NAME	"Manual annotation"

fiji.plugin.trackmate.detection.MaskDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"MASK_DETECTOR"
public static final String	INFO_TEXT	"<html>This detector creates spots from a black and white mask.<p>More precisely, all the pixels in the designated channel that have a value strictly larger than 0 are considered as part of the foreground, and used to build connected regions. In 2D, spots are created with the (possibly simplified) contour of the region. In 3D, a spherical spot is created for each region in its center, with a volume equal to the region volume.<p>The spot quality stores the object area or volume in pixels.</html>"
public static final String	NAME	"Mask detector"

fiji.plugin.trackmate.detection.ThresholdDetectorFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	DETECTOR_KEY	"THRESHOLD_DETECTOR"
public static final String	INFO_TEXT	"<html>This detector creates spots by thresholding a grayscale image.<p>Pixels in the designated channel that have a value larger than the threshold are considered as part of the foreground, and used to build connected regions. In 2D, spots are created with the (possibly simplified) contour of the region. In 3D, a spherical spot is created for each region in its center, with a volume equal to the region volume.<p>The spot quality stores the object area or volume in pixels.</html>"
public static final String	KEY_INTENSITY_THRESHOLD	"INTENSITY_THRESHOLD"
public static final String	KEY_SIMPLIFY_CONTOURS	"SIMPLIFY_CONTOURS"
public static final String	NAME	"Thresholding detector"

fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
protected static final String	BASE_ERROR_MESSAGE	"[SemiAutoTracker] "
protected static final double	NEIGHBORHOOD_FACTOR	2.0

fiji.plugin.trackmate.features.FeatureUtils

Modifier and Type	Constant Field	Value
public static final String	USE_RANDOM_COLOR_KEY	"RANDOM_COLOR"
public static final String	USE_UNIFORM_COLOR_KEY	"UNIFORM_COLOR"

fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer

Modifier and Type	Constant Field	Value
public static final String	DIRECTIONAL_CHANGE_RATE	"DIRECTIONAL_CHANGE_RATE"
public static final String	KEY	"Directional change"

fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer

Modifier and Type	Constant Field	Value
public static final String	DISPLACEMENT	"DISPLACEMENT"
public static final String	KEY	"Edge speed"
public static final String	SPEED	"SPEED"

fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer

Modifier and Type	Constant Field	Value
public static final String	EDGE_COST	"LINK_COST"
public static final String	KEY	"Edge target"
public static final String	SPOT_SOURCE_ID	"SPOT_SOURCE_ID"
public static final String	SPOT_TARGET_ID	"SPOT_TARGET_ID"

fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Edge location"
public static final String	TIME	"EDGE_TIME"
public static final String	X_LOCATION	"EDGE_X_LOCATION"
public static final String	Y_LOCATION	"EDGE_Y_LOCATION"
public static final String	Z_LOCATION	"EDGE_Z_LOCATION"

fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer

Modifier and Type	Constant Field	Value
public static final String	FEATURE	"MANUAL_EDGE_COLOR"
public static final String	KEY	"Manual edge color"

fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	FEATURE	"MANUAL_SPOT_COLOR"
public static final String	KEY	"Manual spot color"

fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer<T extends RealType<T>>

Modifier and Type	Constant Field	Value
protected static final double	RAD_PERCENTAGE	1.0

fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	CONTRAST	"CONTRAST_CH"
public static final String	KEY	"Spot contrast and SNR"
public static final String	SNR	"SNR_CH"

fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	ASPECTRATIO	"ELLIPSE_ASPECTRATIO"
public static final String	KEY	"Spot fit 2D ellipse"
public static final String	MAJOR	"ELLIPSE_MAJOR"
public static final String	MINOR	"ELLIPSE_MINOR"
public static final String	THETA	"ELLIPSE_THETA"
public static final String	X0	"ELLIPSE_X0"
public static final String	Y0	"ELLIPSE_Y0"

fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory<T extends RealType<T> & NativeType<T>>

Modifier and Type	Constant Field	Value
public static final String	AREA	"AREA"
public static final String	CIRCULARITY	"CIRCULARITY"
public static final String	KEY	"Spot 2D shape descriptors"
public static final String	PERIMETER	"PERIMETER"
public static final String	SHAPE_INDEX	"SHAPE_INDEX"
public static final String	SOLIDITY	"SOLIDITY"

fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Branching analyzer"
public static final String	LONGEST_GAP	"LONGEST_GAP"
public static final String	NUMBER_COMPLEX	"NUMBER_COMPLEX"
public static final String	NUMBER_GAPS	"NUMBER_GAPS"
public static final String	NUMBER_MERGES	"NUMBER_MERGES"
public static final String	NUMBER_SPLITS	"NUMBER_SPLITS"
public static final String	NUMBER_SPOTS	"NUMBER_SPOTS"

fiji.plugin.trackmate.features.track.TrackDurationAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track duration"
public static final String	TRACK_DISPLACEMENT	"TRACK_DISPLACEMENT"
public static final String	TRACK_DURATION	"TRACK_DURATION"
public static final String	TRACK_START	"TRACK_START"
public static final String	TRACK_STOP	"TRACK_STOP"

fiji.plugin.trackmate.features.track.TrackIndexAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track index"
public static final String	TRACK_ID	"TRACK_ID"
public static final String	TRACK_INDEX	"TRACK_INDEX"

fiji.plugin.trackmate.features.track.TrackLocationAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track location"
public static final String	X_LOCATION	"TRACK_X_LOCATION"
public static final String	Y_LOCATION	"TRACK_Y_LOCATION"
public static final String	Z_LOCATION	"TRACK_Z_LOCATION"

fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track motility analysis"
public static final String	TRACK_CONFINEMENT_RATIO	"CONFINEMENT_RATIO"
public static final String	TRACK_LINEARITY_OF_FORWARD_PROGRESSION	"LINEARITY_OF_FORWARD_PROGRESSION"
public static final String	TRACK_MAX_DISTANCE_TRAVELED	"MAX_DISTANCE_TRAVELED"
public static final String	TRACK_MEAN_DIRECTIONAL_CHANGE_RATE	"MEAN_DIRECTIONAL_CHANGE_RATE"
public static final String	TRACK_MEAN_STRAIGHT_LINE_SPEED	"MEAN_STRAIGHT_LINE_SPEED"
public static final String	TRACK_TOTAL_DISTANCE_TRAVELED	"TOTAL_DISTANCE_TRAVELED"

fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track speed"
public static final String	TRACK_MAX_SPEED	"TRACK_MAX_SPEED"
public static final String	TRACK_MEAN_SPEED	"TRACK_MEAN_SPEED"
public static final String	TRACK_MEDIAN_SPEED	"TRACK_MEDIAN_SPEED"
public static final String	TRACK_MIN_SPEED	"TRACK_MIN_SPEED"
public static final String	TRACK_STD_SPEED	"TRACK_STD_SPEED"

fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer

Modifier and Type	Constant Field	Value
public static final String	KEY	"Track quality"
public static final String	TRACK_MEAN_QUALITY	"TRACK_MEAN_QUALITY"

fiji.plugin.trackmate.gui.components.CategoryJComboBox<K,V>

Modifier and Type	Constant Field	Value
protected static final String	INDENT	" "

fiji.plugin.trackmate.gui.components.LogPanel

Modifier and Type	Constant Field	Value
public static final String	DESCRIPTOR	"LogPanel"

fiji.plugin.trackmate.gui.wizard.descriptors.ConfigureViewsDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"ConfigureViews"

fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"ExecuteDetection"

fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteTrackingDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"ExecuteTracking"

fiji.plugin.trackmate.gui.wizard.descriptors.InitFilterDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"InitialFiltering"

fiji.plugin.trackmate.gui.wizard.descriptors.LogPanelDescriptor2

Modifier and Type	Constant Field	Value
public static final String	KEY	"LogPanel"

fiji.plugin.trackmate.gui.wizard.descriptors.SpotDetectorDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"ConfigureDetector"

fiji.plugin.trackmate.gui.wizard.descriptors.SpotTrackerDescriptor

Modifier and Type	Constant Field	Value
public static final String	KEY	"ConfigureTracker"

fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor

Modifier and Type	Constant Field	Value
public static final String	PUB1_TXT	"Ershov, D., Phan, MS., Pylv\u00e4n\u00e4inen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1"
public static final String	PUB1_URL	"https://doi.org/10.1038/s41592-022-01507-1"

fiji.plugin.trackmate.io.CSVExporter

Modifier and Type	Constant Field	Value
public static final String	MISSING_STR	"\u00f8"

fiji.plugin.trackmate.io.TmXmlKeys

Modifier and Type	Constant Field	Value
public static final String	ANALYSER_ELEMENT_KEY	"Analyzer"
public static final String	ANALYSER_KEY_ATTRIBUTE	"key"
public static final String	ANALYZER_COLLECTION_ELEMENT_KEY	"AnalyzerCollection"
public static final String	CROP_DETECTION_CHANNEL_ATTRIBUTE_NAME	"detectionchannel"
public static final String	CROP_ELEMENT_KEY	"BasicSettings"
public static final String	CROP_TEND_ATTRIBUTE_NAME	"tend"
public static final String	CROP_TSTART_ATTRIBUTE_NAME	"tstart"
public static final String	CROP_XEND_ATTRIBUTE_NAME	"xend"
public static final String	CROP_XSTART_ATTRIBUTE_NAME	"xstart"
public static final String	CROP_YEND_ATTRIBUTE_NAME	"yend"
public static final String	CROP_YSTART_ATTRIBUTE_NAME	"ystart"
public static final String	CROP_ZEND_ATTRIBUTE_NAME	"zend"
public static final String	CROP_ZSTART_ATTRIBUTE_NAME	"zstart"
public static final String	DETECTOR_SETTINGS_ELEMENT_KEY	"DetectorSettings"
public static final String	DISPLAY_SETTINGS_ELEMENT_KEY	"DisplaySettings"
public static final String	EDGE_ANALYSERS_ELEMENT_KEY	"EdgeAnalyzers"
public static final String	EDGE_FEATURES_ELEMENT_KEY	"EdgeFeatures"
public static final String	FEATURE_ATTRIBUTE	"feature"
public static final String	FEATURE_DECLARATIONS_ELEMENT_KEY	"FeatureDeclarations"
public static final String	FEATURE_DIMENSION_ATTRIBUTE	"dimension"
public static final String	FEATURE_ELEMENT_KEY	"Feature"
public static final String	FEATURE_ISINT_ATTRIBUTE	"isint"
public static final String	FEATURE_NAME_ATTRIBUTE	"name"
public static final String	FEATURE_SHORT_NAME_ATTRIBUTE	"shortname"
public static final String	FILTER_ABOVE_ATTRIBUTE_NAME	"isabove"
public static final String	FILTER_ELEMENT_KEY	"Filter"
public static final String	FILTER_FEATURE_ATTRIBUTE_NAME	"feature"
public static final String	FILTER_VALUE_ATTRIBUTE_NAME	"value"
public static final String	FILTERED_TRACK_ELEMENT_KEY	"FilteredTracks"
public static final String	FRAME_ATTRIBUTE_NAME	"frame"
public static final String	GUI_STATE_ATTRIBUTE	"state"
public static final String	GUI_STATE_ELEMENT_KEY	"GUIState"
public static final String	GUI_VIEW_ATTRIBUTE	"key"
public static final String	GUI_VIEW_ATTRIBUTE_POSITION_HEIGHT	"height"
public static final String	GUI_VIEW_ATTRIBUTE_POSITION_WIDTH	"width"
public static final String	GUI_VIEW_ATTRIBUTE_POSITION_X	"x"
public static final String	GUI_VIEW_ATTRIBUTE_POSITION_Y	"y"
public static final String	GUI_VIEW_ELEMENT_KEY	"View"
public static final String	IMAGE_ELEMENT_KEY	"ImageData"
public static final String	IMAGE_FILENAME_ATTRIBUTE_NAME	"filename"
public static final String	IMAGE_FOLDER_ATTRIBUTE_NAME	"folder"
public static final String	IMAGE_HEIGHT_ATTRIBUTE_NAME	"height"
public static final String	IMAGE_NFRAMES_ATTRIBUTE_NAME	"nframes"
public static final String	IMAGE_NSLICES_ATTRIBUTE_NAME	"nslices"
public static final String	IMAGE_PIXEL_HEIGHT_ATTRIBUTE_NAME	"pixelheight"
public static final String	IMAGE_PIXEL_WIDTH_ATTRIBUTE_NAME	"pixelwidth"
public static final String	IMAGE_TIME_INTERVAL_ATTRIBUTE_NAME	"timeinterval"
public static final String	IMAGE_VOXEL_DEPTH_ATTRIBUTE_NAME	"voxeldepth"
public static final String	IMAGE_WIDTH_ATTRIBUTE_NAME	"width"
public static final String	INITIAL_SPOT_FILTER_ELEMENT_KEY	"InitialSpotFilter"
public static final String	LOG_ELEMENT_KEY	"Log"
public static final String	MODEL_ELEMENT_KEY	"Model"
public static final String	PLUGIN_VERSION_ATTRIBUTE_NAME	"version"
public static final String	ROI_N_POINTS_ATTRIBUTE_NAME	"ROI_N_POINTS"
public static final String	ROOT_ELEMENT_KEY	"TrackMate"
public static final String	SETTINGS_ELEMENT_KEY	"Settings"
public static final String	SPATIAL_UNITS_ATTRIBUTE_NAME	"spatialunits"
public static final String	SPOT_ANALYSERS_ELEMENT_KEY	"SpotAnalyzers"
public static final String	SPOT_COLLECTION_ELEMENT_KEY	"AllSpots"
public static final String	SPOT_COLLECTION_NSPOTS_ATTRIBUTE_NAME	"nspots"
public static final String	SPOT_ELEMENT_KEY	"Spot"
public static final String	SPOT_FEATURES_ELEMENT_KEY	"SpotFeatures"
public static final String	SPOT_FILTER_COLLECTION_ELEMENT_KEY	"SpotFilterCollection"
public static final String	SPOT_FRAME_COLLECTION_ELEMENT_KEY	"SpotsInFrame"
public static final String	SPOT_ID_ATTRIBUTE_NAME	"ID"
public static final String	SPOT_NAME_ATTRIBUTE_NAME	"name"
public static final String	TIME_UNITS_ATTRIBUTE_NAME	"timeunits"
public static final String	TRACK_ANALYSERS_ELEMENT_KEY	"TrackAnalyzers"
public static final String	TRACK_COLLECTION_ELEMENT_KEY	"AllTracks"
public static final String	TRACK_EDGE_ELEMENT_KEY	"Edge"
public static final String	TRACK_ELEMENT_KEY	"Track"
public static final String	TRACK_FEATURES_ELEMENT_KEY	"TrackFeatures"
public static final String	TRACK_FILTER_COLLECTION_ELEMENT_KEY	"TrackFilterCollection"
public static final String	TRACK_ID_ELEMENT_KEY	"TrackID"
public static final String	TRACK_NAME_ATTRIBUTE_NAME	"name"
public static final String	TRACKER_ATTRIBUTE_NAME	"trackername"
public static final String	TRACKER_SETTINGS_CLASS_ATTRIBUTE_NAME	"trackersettingsclass"
public static final String	TRACKER_SETTINGS_ELEMENT_KEY	"TrackerSettings"

fiji.plugin.trackmate.io.TmXmlReader

Modifier and Type	Constant Field	Value
protected static final boolean	DEBUG	true

fiji.plugin.trackmate.tracking.TrackerKeys

Modifier and Type	Constant Field	Value
public static final boolean	DEFAULT_ALLOW_GAP_CLOSING	true
public static final boolean	DEFAULT_ALLOW_TRACK_MERGING	false
public static final boolean	DEFAULT_ALLOW_TRACK_SPLITTING	false
public static final double	DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR	1.05
public static final double	DEFAULT_BLOCKING_VALUE	1d/0d
public static final double	DEFAULT_CUTOFF_PERCENTILE	0.9
public static final double	DEFAULT_GAP_CLOSING_MAX_DISTANCE	15.0
public static final int	DEFAULT_GAP_CLOSING_MAX_FRAME_GAP	2
public static final double	DEFAULT_KALMAN_SEARCH_RADIUS	20.0
public static final double	DEFAULT_LINKING_MAX_DISTANCE	15.0
public static final double	DEFAULT_MERGING_MAX_DISTANCE	15.0
public static final double	DEFAULT_SPLITTING_MAX_DISTANCE	15.0
public static final String	KEY_ALLOW_GAP_CLOSING	"ALLOW_GAP_CLOSING"
public static final String	KEY_ALLOW_TRACK_MERGING	"ALLOW_TRACK_MERGING"
public static final String	KEY_ALLOW_TRACK_SPLITTING	"ALLOW_TRACK_SPLITTING"
public static final String	KEY_ALTERNATIVE_LINKING_COST_FACTOR	"ALTERNATIVE_LINKING_COST_FACTOR"
public static final String	KEY_BLOCKING_VALUE	"BLOCKING_VALUE"
public static final String	KEY_CUTOFF_PERCENTILE	"CUTOFF_PERCENTILE"
public static final String	KEY_GAP_CLOSING_FEATURE_PENALTIES	"GAP_CLOSING_FEATURE_PENALTIES"
public static final String	KEY_GAP_CLOSING_MAX_DISTANCE	"GAP_CLOSING_MAX_DISTANCE"
public static final String	KEY_GAP_CLOSING_MAX_FRAME_GAP	"MAX_FRAME_GAP"
public static final String	KEY_KALMAN_SEARCH_RADIUS	"KALMAN_SEARCH_RADIUS"
public static final String	KEY_LINKING_FEATURE_PENALTIES	"LINKING_FEATURE_PENALTIES"
public static final String	KEY_LINKING_MAX_DISTANCE	"LINKING_MAX_DISTANCE"
public static final String	KEY_MERGING_FEATURE_PENALTIES	"MERGING_FEATURE_PENALTIES"
public static final String	KEY_MERGING_MAX_DISTANCE	"MERGING_MAX_DISTANCE"
public static final String	KEY_SPLITTING_FEATURE_PENALTIES	"SPLITTING_FEATURE_PENALTIES"
public static final String	KEY_SPLITTING_MAX_DISTANCE	"SPLITTING_MAX_DISTANCE"
public static final String	TRACKER_SETTINGS_ALLOW_EVENT_ATTNAME	"allowed"
public static final String	TRACKER_SETTINGS_ALTERNATE_COST_FACTOR_ATTNAME	"alternatecostfactor"
public static final String	TRACKER_SETTINGS_BLOCKING_VALUE_ATTNAME	"blockingvalue"
public static final String	TRACKER_SETTINGS_CUTOFF_PERCENTILE_ATTNAME	"cutoffpercentile"
public static final String	TRACKER_SETTINGS_DISTANCE_CUTOFF_ATTNAME	"value"
public static final String	TRACKER_SETTINGS_DISTANCE_CUTOFF_ELEMENT	"DistanceCutoff"
public static final String	TRACKER_SETTINGS_FEATURE_ELEMENT	"FeatureCondition"
public static final String	TRACKER_SETTINGS_GAP_CLOSING_ELEMENT	"GapClosingCondition"
public static final String	TRACKER_SETTINGS_LINKING_ELEMENT	"LinkingCondition"
public static final String	TRACKER_SETTINGS_MERGING_ELEMENT	"MergingCondition"
public static final String	TRACKER_SETTINGS_SPLITTING_ELEMENT	"SplittingCondition"
public static final String	TRACKER_SETTINGS_TIME_CUTOFF_ATTNAME	"value"
public static final String	TRACKER_SETTINGS_TIME_CUTOFF_ELEMENT	"TimeCutoff"
public static final String	XML_ATTRIBUTE_TRACKER_NAME	"TRACKER_NAME"

fiji.plugin.trackmate.tracking.jaqaman.LAPUtils

Modifier and Type	Constant Field	Value
public static final String	XML_ELEMENT_NAME_FEATURE_PENALTIES	"FeaturePenalties"
public static final String	XML_ELEMENT_NAME_GAP_CLOSING	"GapClosing"
public static final String	XML_ELEMENT_NAME_LINKING	"Linking"
public static final String	XML_ELEMENT_NAME_MERGING	"TrackMerging"
public static final String	XML_ELEMENT_NAME_SPLITTING	"TrackSplitting"

fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	THIS2_INFO_TEXT	"<html>This tracker is identical to the sparse LAP tracker present in this trackmate, except that it <br>proposes fewer tuning options. Namely, only gap closing is allowed, based solely on <br>a distance and time condition. Track splitting and merging are not allowed, resulting <br>in having non-branching tracks. </html>"
public static final String	THIS2_NAME	"Simple LAP tracker"
public static final String	THIS2_TRACKER_KEY	"SIMPLE_SPARSE_LAP_TRACKER"

fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	THIS_INFO_TEXT	"<html>This tracker is based on the Linear Assignment Problem mathematical framework. <br>Its implementation is adapted from the following paper: <br><i>Robust single-particle tracking in live-cell time-lapse sequences</i> - <br>Jaqaman <i> et al.</i>, 2008, Nature Methods. <br><p>Tracking happens in 2 steps: First spots are linked from frame to frame to <br>build track segments. These track segments are investigated in a second step <br>for gap-closing (missing detection), splitting and merging events. <br> <p>Linking costs are proportional to the square distance between source and <br> target spots, which makes this tracker suitable for Brownian motion. <br> Penalties can be set to favor linking between spots that have similar <br> features. <p>Solving the LAP relies on the Jonker-Volgenant solver, and a sparse cost matrix formulation, allowing it to handle very large problems. </html>"
public static final String	THIS_NAME	"LAP Tracker"
public static final String	THIS_TRACKER_KEY	"SPARSE_LAP_TRACKER"

fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	THIS_INFO_TEXT	"<html>This tracker is an extended version of the Kalman tracker, that adds the possibility to customize linking costs and detect track fusion (segments merging) and track division (segments splitting). <p> This tracker is especially well suited to objects that move following a nearly constant velocity vector. The velocity vectors of each object can be completely different from one another. But for the velocity vector of one object need not to change too much from one frame to another. <p> In the frame-to-frame linking step, the classic Kalman tracker infer most likely spot positions in the target frame from growing tracks and link all extrapolated positions against all spots in the target frame, based on the square distance. This advanced version of the tracker allows for penalizing links to spots with different features values using the same framework that of the LAP tracker in TrackMate. Also, after the frame-to-frame linking step, track segments are post-processed to detect splitting and merging events, and perform gap-closing. This is again based on the LAP tracker implementation. </html>"
public static final String	THIS_NAME	"Advanced Kalman Tracker"
public static final String	THIS_TRACKER_KEY	"ADVANCED_KALMAN_TRACKER"

fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	KEY	"KALMAN_TRACKER"
public static final String	NAME	"Kalman tracker"

fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>This tracker is the most simple one, and is based on nearest neighbor <br>search. The spots in the target frame are searched for the nearest neighbor <br> of each spot in the source frame. If the spots found are closer than the <br>maximal allowed distance, a link between the two is created. <br><p>The nearest neighbor search relies upon the KD-tree technique implemented <br>in imglib by Johannes Schindelin and friends. This ensure a very efficient tracking and makes this tracker suitable for situation where a huge number <br>of particles are to be tracked over a very large number of frames. However, <br>because of the naiveness of its principles, it can result in pathological <br>tracks. It can only do frame-to-frame linking; there cannot be any track <br>merging or splitting, and gaps will not be closed. Also, the end results are non-deterministic. </html>"
public static final String	NAME	"Nearest-neighbor tracker"
public static final String	TRACKER_KEY	"NEAREST_NEIGHBOR_TRACKER"

fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	INFO_TEXT	"<html>Choosing this tracker skips the automated tracking step <br>and keeps the current annotation.</html>"
public static final String	NAME	"Manual tracking"
public static final String	TRACKER_KEY	"MANUAL_TRACKER"

fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory

Modifier and Type	Constant Field	Value
public static final String	KEY_IOU_CALCULATION	"IOU_CALCULATION"
public static final String	KEY_MIN_IOU	"MIN_IOU"
public static final String	KEY_SCALE_FACTOR	"SCALE_FACTOR"
public static final String	TRACKER_INFO_TEXT	"<html> This tracker is a simple extension of the Intersection - over - Union (IoU) tracker. <p> <p> It generates links between spots whose shapes overlap between consecutive frames. When several spots are eligible as a source for a target, the one with the largest IoU is chosen.<p> <p> The minimal IoU parameter sets a threshold below which links won\'t be created. The scale factor allows for enlarging (&gt;1) or shrinking (&lt;1) the spot shapes before computing their IoU. Two methods can be used to compute IoU: The <it>Fast</it> one approximates the spot shapes by their rectangular bounding-box. The <it>Precise</it> one uses the actual spot polygon. <p> <p> This tracker works in 2D and 3D. However in 3D, the IoU is computed from the bounding-boxes regardless of the choice of the IoU computation method. The <it>Precise</it> method is not implemented.</html>"
public static final String	TRACKER_KEY	"OVERLAP_TRACKER"
public static final String	TRACKER_NAME	"Overlap tracker"

fiji.plugin.trackmate.util.ImageHelper

Modifier and Type	Constant Field	Value
public static final int	BOTTOM_TO_TOP	1
public static final int	SIDE_BY_SIDE	0

fiji.plugin.trackmate.util.cli.CLIUtils

Modifier and Type	Constant Field	Value
public static final String	CONDA_PATH_PREF_KEY	"trackmate.conda.path"

fiji.plugin.trackmate.util.cli.CondaCLIConfigurator

Modifier and Type	Constant Field	Value
public static final String	KEY_CONDA_ENV	"CONDA_ENV"

fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer

Modifier and Type	Constant Field	Value
public static final String	KEY	"HYPERSTACKDISPLAYER"

fiji.plugin.trackmate.visualization.trackscheme.mxScaledLabelShape

Modifier and Type	Constant Field	Value
public static final String	SHAPE_NAME	"scaledLabel"

fiji.plugin.trackmate.visualization.trackscheme.TrackScheme

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_COLOR	"#FF00FF"
public static final String	INFO_TEXT	"<html>TrackScheme displays the tracking results as track lanes, <br>ignoring the spot actual position. <p>Tracks can be edited through link creation and removal.</html>"
public static final String	KEY	"TRACKSCHEME"