MTrackJ: Manual
Quick Links
| Quick Start Page | MTrackJ Shortcuts | Terms and Conditions |
| Launching and Quitting | MTrackJ Data Structure | Acknowledgments |
| Description of Dialog Buttons | MTrackJ Data File Format | Release Notes |
Launching and Quitting
MTrackJ is launched by selecting it from the Plugins menu of ImageJ. This will open the MTrackJ dialog shown below, which is then associated with the currently active image and visually attached to its window. An image can have only one instance of MTrackJ attached to it, but every image can have its own instance of the program, which enables you to work on multiple images at the same time. The program accepts all image types supported by ImageJ and can also handle HyperStacks and Image5D objects.
At any time, the above dialog window (along with the results and log windows, if open) can be put to front by pressing the F key on the keyboard (when the image window corresponding to the dialog is active). Quitting the program is done by clicking the Close button in the title bar of the dialog.
Below is a description of each of the dialog buttons. Click a button in the above image to move directly to its description. If you prefer to first do a basic tracking session to familiarize yourself a little bit with the program before studying its ins and outs, you are referred to the Quick Start Page.
Description of Dialog Buttons
The first set of buttons deal with the clearing, loading, and saving of tracks.
Causes all tracks to be deleted. It also resets a number of internal variables and counters to bring the program back to its ground state before starting a new tracking session.
Opens a dialog for selecting and loading previously saved tracks. By default, files containing tracks (and settings) saved by MTrackJ have the extension ".mdf" (short for MTrackJ data file). Loading a data file causes all current tracks to be deleted. If you have chosen (see the description of the Options button) to use the track displaying settings (if any) stored in the file, these settings are loaded too and activated. If not, the displaying settings are restored from ImageJ's preferences file or reset to their default values.
Opens a dialog for selecting and importing previously saved tracks. All current tracks are retained and the tracks from the data file are simply added to the set. Only track point coordinates are imported from the data file, and any other information (settings) included in the file is ignored. The imported tracks form a separate cluster, or multiple clusters if they have been saved as such (see the description of the Cluster button for more information on clustering).
If the current tracks are not modified from a previously loaded data file, or if they have not been saved previously (in other words, if the program has no idea where to go), clicking this button will open a dialog for specifying the name of a file to save the tracks and settings to. If the image title permits (that is, if it does not contain special characters that are not allowed by the file system), the dialog will propose a file name, which is the image title appended with the ".mdf" (MTrackJ data file) extension. Once a file name has been specified, it is memorized by the program and used by default for subsequent saving actions. To open the dialog again and change the file name, keep the Alt key down while pressing this button.
Coordinate offsetting: It is possible to apply an offset to the point coordinates while loading, importing, and saving tracks. This may be useful for displaying previously generated tracks in a cropped version of the original image sequence. Coordinate offsets can be specified by keeping the Ctrl key down while pressing the Load, Import, or Save button, which opens the dialog below. Notice that the specified offsets will be applied to all subsequent load, import, and save actions (offsets are remembered separately for each of these actions), until you explicitly put them back to zero again. Also, while the dialog accepts floating-point numbers for all dimensions, for loading and importing the resulting t and c coordinate values are rounded to the nearest integer index in order to allow visualizing the points in the corresponding frame and channel, respectively. See the description of the MTrackJ data file format for more information on how floating-point coordinates are handled.
The following buttons deal with the creation and modification of tracks. Each of the buttons represents a specific mode. At most one mode can be active at any time. The currently active button has its text label shown in red. In order for any of these modes to work, the Point selections tool of ImageJ must be active (as indicated below). This tool is activated automatically when pressing any of the mode buttons of the MTrackJ dialog.
Zooming in or out can be done at any time by pressing, respectively, the + (plus) or - (minus) key (when the image window is active). Scrolling the image canvas can be done by keeping the Space bar down while dragging the mouse. These operations can also be carried out using the standard Magnifying glass and Scrolling tool of ImageJ. However, in that case, you need to manually switch back to the Point selections tool afterwards.
Mode for adding new tracks or continuing existing tracks. A new track is initiated by moving the mouse pointer to a feature of interest in the image sequence and pressing the mouse button. The point is then marked by an overlay shape and (by default) the program automatically shows the next frame. A track is formed by pressing the mouse button at the position of the moving feature in subsequent frames. A track is terminated by double clicking the mouse button (less than 200ms between clicks) or by pressing the Esc key (when the image window is active). The next track is then initiated by moving to another feature of interest in some frame (you may want to rewind the time index first) and repeating the procedure.
To continue an existing (previously finished) track, move the mouse pointer to the track while keeping the Ctrl key down, and the program will highlight that track and append its cluster ID (C) and track ID (T) to the information in the status bar. Pressing the mouse button then causes the track to be activated and the next frame (after the last time index in the track) to be shown. From here on the procedure is the same as for adding new tracks.
Important notes regarding tracking:
Tracking constraints: In principle there is no limit (other than finite computer memory) to the number of tracks and track points that can be registered using the program.
Coordinate indication: When moving the mouse pointer over the image, the coordinates of the current mouse position are displayed in the status bar of ImageJ, along with the corresponding image intensity (I). If the Edit > Options > Display > Interpolate Zoomed Images option of ImageJ is selected, intensities are linearly interpolated. For RGB-images, the intensity is computed as I = 0.3R + 0.6G + 0.1B. By default, the program displays non-calibrated (pixel and index) values (for switching to calibrated indication, see the description of the Displaying button).
Point coordinates: The x and y coordinates (starting at 0) of track points are registered with subpixel precision. The tracking (and displaying) precision of these coordinates is the inverse of the zooming factor: for example, if the image is displayed at 400%, the precision is 1/4th of a pixel, where an integer coordinate value corresponds to the center of a pixel. The t, z, and c coordinates (the latter two are relevant only in the case of multi-channel 3D image sequences) are simply the frame, slice, and channel index, respectively, and are therefore integer valued (starting at 1).
Time stepping: By default, the program shows the next frame of the image sequence after adding a point. If, however, the Shift key is down while pressing the mouse button, it moves to the previous rather than the next frame. This facilitates tracking in time-reversed mode. It is also possible to change the step size, or to switch off automatic time stepping altogether (see the description of the Tracking button).
Time constraints: A track can have only one point in any given frame. If during tracking you return to a frame for which the currently active track has already registered a point, pressing the mouse button in that frame will replace that track point with the newly clicked point.
Channel constraints: In the case of multi-channel 3D image sequences, a track can be in only one channel. That is to say, the c coordinate is the same for all points of a track. This is enforced by the program by copying the c coordinate of the first point of the track to all other points.
Tracking facilities: In some cases it may be helpful to move back and forth in time during tracking to better assess where the object of interest is going. This is facilitated by using the scroll wheel of the mouse (if present) or by using the left/right arrow keys on the keyboard (when the image window is active). If, in the case of (multi-channel) 3D image sequences, the Shift key is down at the same time, the program will browse through the z dimension rather than the t dimension, and if the Ctrl key is down, it will browse through the c dimension. For additional tracking options, see the description of the Tracking button.
Mode for clustering existing tracks. By default, all tracks are added to the default cluster (cluster 1). Move the mouse pointer in the image and the currently active cluster ID (AC) is displayed in the status bar of ImageJ, along with the pointer coordinates and image intensity. If the mouse pointer approaches a track, the program will highlight the track and append its cluster ID (C) and track ID (T) to the information in the status bar. Pressing the mouse button then causes the track to be assigned to the currently active cluster. If the Ctrl key is down while pressing the mouse button, the dialog shown below is opened, which allows specifying the active cluster, which can be an existing cluster or a New cluster.
Any subsequently clicked track is assigned to the lastly selected active cluster. As soon as there is more than one cluster, the program explicitly displays the cluster ID in front of the track ID in the image, in the form C:T.
Mode for (un)hiding tracks or clusters. Move the mouse pointer to the track (default) or cluster (Shift key down while moving) to be hidden, and the program will highlight that object and append its cluster ID (C) and track ID (T) (whichever of these are applicable) to the information in the status bar. Pressing the mouse button then causes the object to be made invisible, but not deleted. Conversely, if the Ctrl key is down while pressing the mouse button, all tracks except the highlighted one(s) will be made invisible. This allows to temporarily exclude (or keep only) specific tracks or clusters for a presentation (see the description of the Movie button on how to make movies) or in making measurements (see the description of the Measure button). Hidden tracks are all made visible again by keeping the Ctrl key down and pressing either the mouse button in an empty area (not containing tracks) in the image, or the Hide button of the dialog. If, in addition to the Ctrl key, the Alt key is also down, the visibility of all tracks is inverted (all hidden tracks are made visible again while all visible tracks are hidden).
Mode for changing the colors of tracks. Move the mouse pointer to a track, and the program will highlight that track and append its cluster ID (C) and track ID (T) to the information in the status bar of ImageJ. Pressing the mouse button then opens the dialog shown below.
Move the mouse pointer over the colors in the dialog, and the program will list the color in the status bar, in the form (R,G,B) (press the Ctrl key while the dialog is active to see the numbers in hexadecimal form). Pressing the mouse button at any of the colors causes that color to be assigned to the highlighted track. This mode can also be used to set the colors of clusters, or of the entire assembly of clusters, if you have selected, respectively, the Per cluster or Monochrome coloring scheme, rather than the Per track coloring scheme, in the dialog associated with the Displaying button.
Mode for deleting points, tracks, or entire clusters. Move the mouse to the point (default), or track (Ctrl key down while moving), or cluster (Ctrl+Shift keys down while moving) to be deleted, and the program will highlight that object and append its corresponding cluster ID (C), track ID (T), and point ID (P) (whichever of these are applicable) to the information in the status bar of ImageJ. In the case of points, the program will also display this information in the image, in the form C:T:P (where the C: part is suppressed if there is only one cluster), and it will move the image to the time index, and, in the case of (multi-channel) 3D image sequences, also the slice and channel index, corresponding to that point. Pressing the mouse button then deletes the highlighted object.
Mode for moving points, tracks, or entire clusters. Move the mouse pointer to the point (default), or track (Ctrl key down while moving), or cluster (Ctrl+Shift keys down while moving) to be displaced, and the program will highlight that object and append its corresponding cluster ID (C), track ID (T), and point ID (P) (whichever of these are applicable) to the information in the status bar of ImageJ. In the case of points, the program will also display this information in the image, in the form C:T:P (where the C: part is suppressed if there is only one cluster), and it will move the image to the time index, and, in the case of (multi-channel) 3D image sequences, also the slice and channel index, corresponding to that point. Dragging the mouse then moves the highlighted point, track, or cluster. Note that only the x, y, and (if applicable) the z coordinate (slice index) can be changed. The t coordinate (time index) and the c coordinate (channel index) of the moved objects will remain untouched.
Mode for merging existing tracks, two at a time. Move the mouse pointer to the first track, and the program will highlight that track and append its cluster ID (C) and track ID (T) to the information in the status bar of ImageJ. Pressing the mouse button then causes the track to be selected as the base track for merging (click the track again if you need to deselect it). Move the mouse pointer to highlight another track (again, the corresponding cluster ID (C) and track ID (T) are displayed in the status bar), and click the mouse button to complete the merging operation.
Since a track can have only one point per frame, any point in the base track for which there exists a point in the secondly clicked track having the same t coordinate (time index) is replaced by the latter (in the extreme case, when there is full time-overlap, the base track gets completely replaced by the secondly clicked track). Also note, in the case of (multi-channel) 3D image sequences, that since a track can be in only one channel, the c coordinates (channel indices) of the points in the merged track are explicitly set to the channel index of the base track.
Mode for splitting an existing track at a given point. Move the mouse pointer to the point at which the track should be split, and the program will highlight that point and append its cluster ID (C), track ID (T), and point ID (P) to the information in the status bar of ImageJ. The program will also display this information in the image, in the form C:T:P (where the C: part is suppressed if there is only one cluster), and it will move the image to the time index, and, in the case of (multi-channel) 3D image sequences, also the slice and channel index, corresponding to that point. pressing the mouse button then causes the track to be split at that point into two separate tracks. The first track consists of all points from the first point of the original track up to (not including) the clicked point. The second track consists of all points from the clicked point to the last point (inclusive) of the original track. If the Ctrl key is down while pressing the mouse button, (a copy of) the clicked point is included in both the first and the second track.
Mode for setting the reference. The reference is a single landmark point in the image, with respect to which distances can be measured (see the description of the Measure button for more on measuring tracks). Move the mouse pointer in the image to the x and y coordinate (and the z coordinate in the case of (multi-channel) 3D image sequences) corresponding to a point of interest. Pressing the mouse button then causes this point to be marked as the reference. The reference point is always displayed highlighted. To reset the reference, simply press the mouse button at some other position of interest in the image (the point cannot be moved in the same fashion as track points).
Mode for setting (changing) the ID numbers of objects (points, tracks, or entire clusters). Any object is assigned a (unique) ID only at the time of its creation. Some operations may introduce gaps in the ID numbers (such as, for example, when a point is deleted from the middle of a track, or a track is deleted from a cluster). To manually change ID numbers (see below for automatic renumbering), move the mouse to the point (default), or track (Ctrl key down while moving), or cluster (Ctrl+Shift keys down while moving) to be renumbered, and the program will highlight that object and append its corresponding cluster ID (C), track ID (T), and point ID (P) (whichever of these are applicable) to the information in the status bar of ImageJ. In the case of points, the program will also display this information in the image, in the form C:T:P (where the C: part is suppressed if there is only one cluster), and it will move the image to the time index, and, in the case of (multi-channel) 3D image sequences, also the slice and channel index, corresponding to that point. Pressing the mouse button then opens the dialog below (with the word Point replaced by Track or Cluster where applicable), which shows the current ID number and allows specifying a new number.
The ID number must be an integer larger than zero. If the entered number is already in use by another object, for example by another point of the same track (when setting a point ID), or by another track of the same cluster (when setting a track ID), or by another cluster of the assembly (when setting a cluster ID), the IDs of the two objects are interchanged. To automatically reassign consecutive ID numbers to all objects, keep the Ctrl key down while pressing this button. This works regardless of whether the ID mode is active.
The following buttons deal with measuring tracks and making movies.
Before measuring tracks, please make sure that the pixel calibration is properly set. This is checked by opening the Image > Properties dialog of ImageJ (you need to consider only the Unit of Length, Pixel Width, Pixel Height, Voxel Depth, and Frame Interval fields in this dialog). If necessary, intensity calibration (only for 8-bit and 16-bit images) can be set in the Analyze > Calibrate dialog of ImageJ.
Pressing the button then immediately causes the program to perform prespecified measurements. To specify the type of measurements to be performed and displayed, keep the Ctrl key down while pressing the button, which opens the dialog below (see the description of the MTrackJ data structure to understand the terminology used here).
Display point measurements: Option to display or hide point measurement results. The corresponding results window (see below) displays a number of basic measurements on a point-by-point basis.
Display track measurements: Option to display or hide track measurement results. The corresponding results window displays for each track the minimum, the maximum, the mean, and the standard deviation of the point measurements for the track (for those measures for which these statistics make sense). In addition, it displays the number of points, the total duration, the total length, and the channel number for each track.
For some measures, the sample size for a track, that is the number of valid point measurements available for the track, may be less than the total number of points in the track. For example, there is no speed measurement for the first point of any track (marked by NA in the point measurements window shown below), and hence the sample size for computing the speed statistics of a track is one less than the number of points in the track.
Display cluster measurements: Option to display or hide cluster measurement results. The corresponding results window displays for each cluster the minimum, the maximum, the mean, and the standard deviation of all point measurements for the cluster (for those measures for which these statistics make sense). In addition, it displays the number of tracks and points in each cluster, as well as the minimum, the maximum, the mean, and the standard deviation of the durations and the lengths of the tracks in the cluster.
For each measure (except duration and length), the mean and the standard deviation of a cluster are computed as the weighted mean and standard deviation of the corresponding track measurements, where the weight for each track is equal to the number of points in the track. This is the same as computing the uniformly weighted mean and standard deviation of the pooled point measurements.
Display assembly measurements: Option to display or hide assembly measurement results. The corresponding results window displays for the entire assembly the minimum, the maximum, the mean, and the standard deviation of all point measurements (for those measures for which these statistics make sense). In addition, it displays the number of clusters, tracks, and points, as well as the minimum, the maximum, the mean, and the standard deviation of the durations and the lengths of all tracks in the assembly.
The assembly mean and standard deviation of any measure (except duration and length) are computed from the pooled point measurements. The mean and standard deviation of the duration and length measures are computed from the corresponding (pooled) track measurements.
Include all tracks in measurements: Option to include all tracks in performing measurements. If not selected, measurements are performed only for tracks that are visible (at any time point), excluding hidden tracks and tracks that are not visible in the present channel.
Maximum decimal places: The maximum number of decimal places with which floating-point numbers are displayed in the result windows. That is, numbers that would require more decimal places for exact representation, are rounded to the specified number of decimal places.
Pressing the OK button in the measurements dialog starts the selected measurements. The result windows are automatically put to front every time this button is pressed. At any time, the result windows (along with the main dialog and the log window) can also be put to front by pressing the F key on the keyboard (when the image window is active).
An example of a point measurement results window is given below. The listed numbers can be saved to disk using the File > Save As menu option of the window. The resulting (tab-delimited) file can then be imported in any spreadsheet program.
A brief description of the quantities listed:
Nr: The measurement number. Runs from 1 to the total number of points.
CID: The ID number of the cluster to which the track point belongs. This quantity is not displayed if there is only one cluster and the user has deselected the displaying of cluster and assembly measurements.
TID: The ID number of the track to which the point belongs.
PID: The ID number of the point.
x [unit]: The calibrated x coordinate of the point. The pixel width and unit of length used here can be set as described above.
y [unit]: The calibrated y coordinate of the point. The pixel height and unit of length used here can be set as described above.
z [unit]: The calibrated z coordinate of the point. The voxel depth and unit of length used here can be set as described above. This quantity is not displayed in the case of 2D image sequences.
t [unit]: The calibrated t coordinate of the point. The frame interval and unit of time used here can be set as described above.
c [idx]: The channel index of the point. This quantity is not displayed if there is only one channel.
I [unit]: The calibrated image intensity value at the point. For 8-bit and 16-bit images, the intensity calibration function and value unit can be set (if necessary) as described above. For RGB-images, the intensity is computed as I = 0.3R + 0.6G + 0.1B. If the Edit > Options > Display > Interpolate Zoomed Images option of ImageJ is selected, the (calibrated) intensities are linearly interpolated where necessary (subpixel coordinate precision).
Len [unit]: The length of the track from the start (first) point of the track to the current point (inclusive). Thus the value of this quantity for the end (last) point of a track equals the total length of the track. The pixel calibration and unit of length used here can be set as described above.
D2S [unit]: The distance from the start (first) point of the track to the current point. Thus the value of this quantity is always less than (or at most equal to) the value of Len. The pixel calibration and unit of length used here can be set as described above.
D2R [unit]: The distance from the current point to the reference point (see the description of the Refer button for information on how to set the reference). The pixel calibration and unit of length used here can be set as described above.
D2P [unit]: The distance from the current to the previous point of the track. The pixel size and unit of length can be set as described above.
v [unit]: The speed, at the current point, of the object represented by the track. This quantity is computed as the magnitude of the most recent displacement vector (pointing from the previous point to the current point of the track), divided by the frame interval. The pixel calibration, unit of length, frame interval, and unit of time can be set as described above.
α [deg]: The angle of the in-plane component of the most recent displacement vector (pointing from the previous point to the current point of the track) with respect to the x-y coordinate system of the image (with the origin taken in the previous point). Angle values range from -180 to +180 degrees, where 0 degrees means the vector component runs parallel to the positive x axis (pointing to the right), +90 degrees (or -90 degrees) means it runs parallel to the positive (or negative) y axis (pointing downward, or upward, respectively), and +180 degrees (which is the same as -180 degrees) means it runs parallel to the negative x axis (pointing to the left). The pixel calibration can be set as described above.
Δα [deg]: The angular change between the in-plane components of the most recent displacement vector (pointing from the previous point to the current point of the track) and the preceding displacement vector. The pixel calibration can be set as described above.
θ [deg]: The angle of the most recent displacement vector (pointing from the previous point to the current point of the track) relative to the x-y plane of the image (with the origin taken in the previous point). The angle values range from -90 to +90 degrees, where 0 degrees means the axial vector component is zero (that is, the displacement vector is entirely in-plane), and +90 degrees (or -90 degrees) means it runs parallel to the positive (or negative) z axis (pointing away from, respectively toward, the observer). The pixel calibration can be set as described above. This quantity is not displayed in the case of 2D image sequences.
Δθ [deg]: The angular change between the most recent displacement vector (pointing from the previous point to the current point of the track) and the preceding displacement vector, relative to the x-y plane of the image. The pixel calibration can be set as described above. This quantity is not displayed in the case of 2D image sequences.
Measurements for which no sensible value can be determined are marked by NA. For example, for D2R this is the case if the reference point has not been set, and for D2P, v, α, and θ this is always the case for the first point of a track (which has no previous point), and for v this is also the case if the frame interval is zero (which would otherwise result in a division by zero in the calculations).
All graphical objects (track points, connecting lines, ID numbers) are displayed in overlay mode and never become part of the original image data. Pressing the button starts the module for generating a movie (RGB-color type) containing the frames with the tracks drawn into them. Thus the resulting movie is a "hardcopy" of what you see when moving the time index (scroll bar) of the original image window. This movie can then be saved to disk, for example using the File > Save As > AVI menu item of ImageJ (or a plugin for exporting to some other format), and used later in presentations. The track displaying behavior is highly configurable (see the description of the Displaying button).
Note that in the case of (multi-channel) 3D image sequences, it is naturally impossible to display the correct slice and channel for all track points at the same time index, if there are multiple tracks. Therefore, the slice and channel indices used for movie generation in such cases are fixed to the values of the image window at the time the button is pressed. The only exception to this rule is when there is only a single track. In that case, since there can be only one point per time index, the resulting movie will display the slice and channel corresponding to each point.
By default, the generated movie has the same duration (number of frames) as the input image sequence. However, keeping if the Ctrl key down while pressing the button opens the dialog below, which allows to refine the movie.
Trim movie to all-first and all-last track points: Option to delete or keep the leading and trailing frames of the movie that do not contain track points.
Drop frames for which there are no track points: Option to delete or keep all frames of the movie that do not contain track points.
The movie production module runs in a separate thread in order for ImageJ to remain responsive. It is, however, not possible to edit tracks or their displaying settings during movie production.
The final set of buttons allow configuring the tracking, displaying, and general program behavior, and opening this online manual.
Opens the dialog below for configuring the tracking behavior of the program. The selected tracking options are activated when pressing the OK button of the dialog. They are also stored in ImageJ's preferences file and loaded when restarting the program.
A brief description of the options:
Move to next time index after adding point: Option to let the program automatically move to the next time index after adding a track point. If the Shift key is down during tracking, it will move to the previous rather than the next time index. This facilitates tracking in time-reversed mode.
Time step size: The step size (in frames) used by the program in moving to the next (or previous) time index. This must be an integer number but may be positive (to move forward in time) or negative (to move backward in time).
Finish track after adding point at last time index: Option to let the program automatically finish (terminate) a track after adding a point in the last (by default) or the first (when the Shift key is down) frame of the image sequence.
Reset time to last start index after finishing track: Option to let the program automatically return to the time index corresponding to the firstly added point of a track, after finishing the track.
Apply local cursor snapping during tracking: Option to let the program automatically pick the position of the specified image feature within the specified window around the current cursor (mouse pointer) position, rather than the cursor position itself, when adding a track point. This option can be temporarily switched off during tracking by keeping the Ctrl key down (when the image window is active).
Snap feature: The image feature to snap the cursor to. Currently this can be either the highest (Maximum intensity) or the lowest (Minimum intensity) value within the snap window, or the intensity-weighted mean position of pixels having a value above (Bright centroid) or below (Dark centroid) a certain threshold. The threshold, which is automatically computed, is the value that maximizes the interclass variance between object and background pixels (also known as Otsu's threshold). Note that snapping operates on the original image intensity values (it ignores possible intensity calibrations). During tracking, the position of the selected snap feature is indicated by a second, smaller crosshair cursor (in highlighting color), next to the normal cursor.
Snap range: The size (in pixels) of the window within which the program searches for the snap feature position. During tracking, this window is indicated by a dotted square (in highlighting color) around the cursor position. The currently supported window sizes range from 3x3 to 51x51 pixels. The size always consists of odd numbers to have an equal number of pixels on either side of the pixel corresponding to the current position.
Opens the dialog below for configuring the displaying behavior of the program. The selected displaying options are activated when pressing the OK button of the dialog. They are also stored in ImageJ's preferences file and loaded when restarting the program.
A brief description of the options:
Display reference: Option to display or hide the reference point, if set (see the description of the Refer button for defining the reference).
Display active track: Option to display or hide the currently active (not yet finished) track.
Display finished tracks: Option to display or hide the finished tracks. This may be helpful if you do not want to be distracted by these tracks while creating a new track.
Visibility: Determines which part of the tracks is visible. This can be the Entire track (tracks are always drawn from start to end point, regardless of the current time index), or Up to current time (tracks are drawn up to and including the current time index), or From current time (tracks are drawn starting from the current time index until the end of the track). The latter mode may be useful in time-reversed tracking applications.
Coloring: The coloring scheme used for drawing tracks. Tracks can be drawn with a different color Per track, or with the same color Per cluster, or all with the same Monochrome color. In each mode, the visible color of an object (track, cluster, all) can be changed as needed (see the description of the Color button). Note that the program has a limited color palette, currently consisting of 100 different colors (gray values not included). If there are more than this number of objects requiring a color, the program will start reusing colors.
Background: The background filling scheme used. This can be the original Image or a uniform White, Gray, or Black background.
Highlighting: The color used for highlighting objects. This is also the color used for drawing the reference point (if set) and the snap window and cursor (when used). Only a limited set of standard colors can be selected.
Opacity: The opacity (in percent) of the drawn tracks. Possible values run from 0 to 100 percent, with steps of 5 percent. An opacity of 100 percent means that wherever tracks are drawn, the background (the image or a uniform fill) is invisible. An opacity of 70 percent means that the tracks and the background are blended, at a ratio of 70 to 30 percent. An opacity of 0 percent means that tracks are not visible.
Point size: The size (in pixels) with which track points are drawn. The currently available (even) values run from 0 to 100 pixels. A point size of 0 pixels means that points are not drawn.
Point shape: The shape used for drawing track points. The currently available shapes are Circle, Square, Triangle, and Cross. For each of these shapes, a one-pixel dot is drawn in the center, which more accurately indicates the real position of the point.
Point style: The style used for drawing track points. This can be either Open or Closed. This option is irrelevant for the Cross point shape.
Point coding: The depth coding used for drawing track points. This can be None (all points are drawn with the same size and color), Depth > size (where for each point, the size depends on the z index of the point, ranging from the specified Point size if z equals 1, linearly reducing to 10 percent of the Point size if z equals the number of slices), Depth > color (where for each point, the color depends on the z index of the point, according to the spectrum below, which ranges from red if z equals 1, to blue if z equals the number of slices), Depth > both (where for each point, both size and color coding is applied, as described), and the same series of options for Distance (where for each point, the size or color depends on the distance of the z index of the point, to the z index of the currently shown image slice).
Track width: The width (in pixels) of the lines connecting the track points. The currently available values run from 0 to 100 pixels. A width of 0 pixels means that the lines are not drawn.
Track IDs: The position along the track where the track ID numbers are drawn. The currently available positions are Tail, Head, and Middle.
Font size: The size (in pixels) with which ID numbers are drawn. The currently available values run from 0 to 100 pixels. A font size of 0 pixels means that ID numbers are not drawn.
Font style: The style with which ID numbers are drawn. The currently available font styles are Plain, Bold, Italic, and Italic-Bold.
Display only tracks present in current channel: Option to display only those tracks having a channel index equal to the current channel. This option applies only to (multi-channel) 3D image sequences.
Display only tracks present at current time: Option to display only those tracks having a point corresponding to the current time index. This may be helpful if there are many tracks and you want to see only those being present at the current time.
Display only track points at current time: Option to draw the selected point shape only for those points corresponding to the current time index. This allows (for example) displaying the track up to the current time, with only the current time point being drawn.
Display calibrated coordinates and values: Option to display calibrated coordinate and image intensity values rather than non-calibrated (pixel and index) values in the status bar of ImageJ (as well as in the log window of MTrackJ) when moving the mouse pointer over the image.
Opens the dialog below for configuring the general program behavior. The selected program options are activated when pressing the OK button of the dialog. They are also stored in ImageJ's preferences file and loaded when restarting the program.
A brief description of the options:
Display log messages: Option to display or hide the log messages generated by the program. All operations generate log messages explaining in some more detail what is happening. This also allows you to exactly reconstruct the track generation process afterwards. The text in the log window can be saved to disk using the File > Save As menu option of the window. At any time, the log window (along with the dialog and results windows) can be put to front by pressing the F key on the keyboard (when the image window is active).
Operate in safe modification mode: Option to enable or disable safe modification of tracks. If this option is selected, the program will ask for confirmation for each destructive modification of tracks. This option was introduced because the program has no undo functionality.
Use displaying settings from data files: Option to enable or disable using the stored displaying settings when loading data files. When saving tracks to a data file (using the Save button), the current displaying settings (as shown in the dialog associated with the Displaying button) and track colors are also stored in the file, along with the tracks. If this option is selected, these settings are restored and activated when loading the data file again. If not, the program will ignore these settings and continue using the current displaying settings.
Activate image window when mouse enters: Option to enable or disable automatic image activation when the mouse pointer enters the image window. The image window needs to be active in order for the key bindings to work. If this option is not selected, the user will need to manually activate the window first (either by pressing its title bar or by clicking in the window) to enable the key bindings.
Move main dialog along with image window: Option to enable or disable the automatic displacement of the main dialog window when the image window is moved. If this option is selected, the dialog window always keeps the same position relative to the image window.
Separate folders for loading/importing/saving: Option to enable or disable the separate memorization of the lastly visited folders for loading, importing, and saving data files. If this option is selected, the file dialogs associated with the Load, Import, and Save buttons will open in their respective lastly visited folder. If this option is not selected, these dialogs will open in the same folder (the folder lastly visited by any of the three).
Reuse last file folders from previous session: Option to enable or disable setting the initial folders for loading, importing, and saving files to the lastly visited folders in the previous session. If this option is selected, the program will store the paths in ImageJ's preferences file when quitting, and reuse them as initial folders for the file dialogs associated with the Load, Import, and Save buttons when the program is started again.
Ask to save changes before loading or quitting: Option to enable or disable the request to save changes (introduced since the last save action) when loading a new data file or quitting the program.
Ask for confirmation before quitting program: Option to enable or disable the request for confirmation when quitting the program (by pressing the Close button in the title bar of the dialog).
Opens the default internet browser showing this online manual.