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TrackMate version history

6,034 bytes added, 08:25, 5 September 2019
06/09/2019 - v4.0.1
* Semi-automatic tracking: Select one (or more) spot, TrackMate will find its most likely successors.
* Re-design of TrackScheme. TrackScheme is now about 40 times faster to launch, even on large dataset. By default it uses the 'simple' style, and the update of the small thumbnails can be switched on/off.
* The 'Load' button was removed from the GUI. TrackMate files can be loaded from the ''{{bc | Plugins > | Tracking > | Load a TrackMate file'' }} menu item.* T/here is a new ''{{bc | Plugins > | Tracking > | Manual tracking with TrackMate'' }} menu item, that launched another GUI stripped down for manual editing.
* The XML file format has changed, to include more data, and for better separability and reuse in other softwares. However, backward compatible loaders are present to ensure the loading and on-the-fly conversion with files generated by TrackMate versions above 1.2.
* Better coloring scheme. There is a unique coloring scheme shared in all views.
* The user can now define a ''depth of drawing'' display setting, that limits the number of Z-slices on which we draw the model. This is useful on very thick samples where the drawing of all the data across all Zs can become confusing.
* Minor improvement for the track display on the main view, for large models.
* Ship a [[MATLAB ]] function to import in [[MATLAB ]] the tracks exported by TrackMate. Check [[Using_TrackMate_with_MATLAB|this]].
* Warn the user if they feed TrackMate with a stack that has no time-points by plenty of Z-slices. This is one of the main reason we get irrelevant bug reports: By default, ImageJ considers that a multi-image file is always made of 1 time-points and many Z-slices. Whereas users mean to feed TrackMate with a movie made of several 2D planes filmed over time. We now warn the user that the dimensionality stored in the image might not be the one they expect.
* '''Fine tune multithreading'''. Before this version, TrackMate was doing multithreading during detection in the following way: We run the detection process on as many frames as we have threads, and each frame is processed using 1 thread. This is suboptimal if we have a large number of threads, but a few number of frames (e.g. 1 frame, 24 threads). This release fixes this: If we have 10 threads and 15 frames to process, we process 10 frames at once, and allocate 1 thread per frame. But if we have 10 threads and 2 frames, we process the 2 frames at once, and allocate 5 threads per frame if we can. For this to work of course, the detector must be multithreaded, which is the case with the ones we ship now.
* It is possible to manually color spots and edges. The colors attributed are saved and retrieved from XML. To use it, select a few cells in TrackScheme and right-click to make the contextual menu appear:
* There is now an action to export to [http://icy.bioimageanalysis.org/ Icy] track manager. It generates a XML file that can be opened in the [http://icy.bioimageanalysis.org/plugin/Track_Manager Icy track manager].
* Icy XML track files can be opened in TrackMate. Just point the TrackMate loader plugin to such a file, and its type will be detected and it will be opened in TrackMate. We would like to express our thanks to [http://icy.bioimageanalysis.org/about Fabrice de Chaumont] {{Person|Fab14}} for his help in developing these two features.
* A new action allows merging two TrackMate files into one.
* The color scale used to display colored tracks, links and spots can now be manually adjusted. In the display panel of the GUI, double click on the label "color by" and a settings window will open allowing the user to select between manual or automatic scaling. This is great to generate views that are comparable between datasets. This feature is commissioned and offered by Fumio Hayashi, Kobe University.
* Add a new tracking algorithm: [[TrackMate_algorithms#Linear_motion_tracker|the linear motion LAP tracker]].
 
== 26-01-2015 - v2.7.2 ==
* Fix a bug in the Linear motion LAP tracker, noticed by Ronny Sczech. The bug caused the linear tracker to crash on some cases.
 
 
== 19-03-2015 - v2.7.3 ==
 
* Fix a bug introduced by recent changes in the imglib2-algorithm, noticed by several people, and that prevented any spot feature to be computed.
 
 
== 23-06-2015 - v2.7.4 ==
 
* Fix a bug, incorrectly fixed in imglib, that caused dead threads to accumulate upon running the detection step. Noticed and fixed by @hadim, @dietzc and @tpietzsch.
 
== 27-10-2015 - [[2015-10-27_-_TrackMate_v2.8.0_released|v2.8.0]] ==
 
* Contributed modules.
** Ronny Sczech linear tracker and batch modules.
** Thorsten Wagner Find maxima detector.
** Benoit Lombardo analyzers.
* Improvements.
** Faster track rendering.
** The ROI edit tool.
** The Block LoG detector.
** TrackMate honors ImageJ thread configuration.
** TrackScheme acknowledges the spot radius setting when capturing thumbnails.
** The Extract track stack action improved.
** A new action to prune filtered out data.
** The Quality value reported by the LoG detector is now sensible.
* Bugfixes.
** Fix the accuracy problem in sub-pixel localization.
** Fix the huge delay when manually adding a spot to large models.
** The median filter was crashing TrackMate for 3D images.
 
== 07/11/2015 - v2.8.1 ==
 
* Fix a big causing tracks not to be displayed on Windows platforms.
 
 
 
== 24/03/2016 - v3.0.1 ==
 
 
This major version change only reflects recent changes in TrackMate API, partly prompted by the overhaul in progress in the Fiji ecosystem. There is very little new features and bug fixes and this release will be mainly of use for project depending on TrackMate.
 
Improvements.
* The semi-auto tracker now detects spots in the currently selected channel, in case of a multi-C image.
* The thumbnail images in TrackScheme are taken from the currently selected channel as well.
* There is now a step-wise time browsing ('à la MaMuT'): press 'F' and 'G' to move in time by jumping to frames, spaced by a number set in the Spot edit tool of TrackMate (double-click on the icon in the ImageJ toolbar).
* TrackMate is now more verbose when doing manual editing.
 
Fixes.
* Minor usability fixes.
 
Changes.
* The 3D Viewer is working again, at least (as of today) on Windows platforms. On Macs, the time slider does not work and trying to interact with it will crash Fiji.
* Also, to keep the 3D Viewer tidy, it is not kept in sync with the manual edits made on the model. It just shows a snapshot of the model at the time when it was launched. It was not working properly before anyway, so we officially disable this feature.
 
 
 
== 31/03/2016 - v3.1.0 ==
 
Improvements:
 
* Add an action that export all visible spots statistics, regardless of whether they belong in a track or not.
 
* New display mode: show only selection.
 
This track display mode only shows the content of the current selection, for spots and edges. It can be accessed in the GUI panel 'Configure views' with a special track display mode called 'Selection only'.
 
Careful: the content of the selection model can still be edited in this mode. Of course, the track display mode is ignored by TrackScheme, which then can be used to modify the selection in this mode.
 
Changes:
 
* We really do not relaunch TrackScheme automatically when loading a TrackMate file.
 
 
== 12/04/2016 - v3.2.0 ==
 
* TrackMate can now be called from an IJ macro.
Only a subset of TrackMate features can be used, though. Right now, only the LoG detector and the Simple LAP tracker are used. But for instance, you can call TrackMate with the following syntax:
 
<pre>run('TrackMate', "use_gui=false "
+ "save_to=[/Users/tinevez/Desktop/TrackMateSaveTest.xml] "
+ "export_to=[/Users/tinevez/Desktop/TrackMateExportTest.xml] "
+ "display_results=true "
+ "radius=2.5 "
+ "threshold=50.1 "
+ "subpixel=false "
+ "median=false "
+ "channel=1 "
+ "max_frame_gap=0" )</pre>
 
If you need other detectors and trackers, you have to rely on Python for now. [[Scripting_TrackMate]]
 
* Several TrackScheme improvements:
** The row and column headers are now properly displayed and resized when zooming.
** TrackScheme can be navigated with the keyboard:
*** The numeric keypad is used to pan around.
*** +/- zoom in/out.
** Better navigation with mouse:
*** Hold space and drag to pan, as in ImageJ.
*** Hold space + mousewheel to zoom in/ out.
 
 
== 23/03/2017 - v3.5.0 ==
 
* The '''Recalculate features''' action now recomputes all features.
 
And if a Controller instance is provided, the analyzers declared in the GUI are used to recompute the features. This is useful if a file was saved before new feature analyzers were added.
 
* GUI tweaks.
 
* Allow spot detection on images with a discontinuous ShapeRoi.
If the current ROI is an ij.gui.ShapeRoi, we use this to filter the spot detections in each frame. For other cases, we keep the settings.polygon for backward compatibility. Contributed by Jan Eglinger.
 
* Switch from Jenkins to Travis CI.
By Curtis Rueden.
 
* The Extract track stack action can capture 3D stacks.
 
* Fix Kalman tracker bug for empty first frames.
 
The Kalman tracker was unable to process if the first two frames contained zero spots.
Noted by Hadrien Mary.
 
* Fix improper image factory for very large images.
Noted by Christian Tischer.
 
== 25/06/2018 - v3.8.0 ==
 
* As advised by @ctrueden: do not use java.awt.Robot for capture, but instead directly paint into a BufferedImage. The capture is now much quicker (as fast as painting, no need to wait), more robust, and the code as fewer lines as well. It is so perfect that I wonder why I could not think of this before.
 
* Set the calibration properly, even if this is a capture.
 
* And give a better title to the imp.
 
== 06/09/2019 - v4.0.1 ==
 
* Properly use the ManualDetectorFactory in scripts: does not crash nor remove existing spots.
 
* Display the true plugin version on the GUI. It was displaying 3.8.0 but we were on 4.0.0 for quite some time.
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