TrackMate version history

Revision as of 06:40, 5 August 2013 by JeanYvesTinevez (talk | contribs) (v2.1.0)

This page contains the version history for the TrackMate plugin. Bug fixes are not mentioned here, and do not get their own release number.

10/05/2012 - v.1.0

Initial release

22/05/2012 - v1.1

  • TrachScheme can change of display style.
  • De-activated folding branches in TrackScheme, as it was non-functional.
  • Fix bugs when loading invisible tracks.

13/06/2012 - v1.2

  • Far better memory management and speed improvement in LAP trackers when dealing with gap-closing only.
  • Renamed the "Fast LAP tracker" and "Simple Fast LAP tracker" to "LAP tracker" and "Simple LAP tracker". Also removed the old "LAP tracker" and "Simple LAP tracker". They give the same results, but are just way slower.
  • Replaced the ISBI challenge exporter by a simple track exporter.
  • New action: capture the spot images along a track.

25/02/2013 - v2.0.0

Major update:

  • TrackMate now uses ImgLib2 internally, and is therefore ready to be moved to ImageJ2.
  • TrackMate now computes edge features (on top of spot and track features). These features enable the immediate measure of velocity, displacement, etc...
  • Tracks can be colored in the Hyperstack displayer, in the 3D viewer and in TrackScheme using indifferently track or edge features.
  • All spot, edge and track features are computed automatically and kept in sync even versus manual modifications.
  • All spot, edge and track features are saved in the XML file.
  • All spot, edge and track features can be exported as ImageJ results tables. Then they can be exported to text files, readable by let's say Excel. (Please note that the authors of the plugin do not deem Excel as a proper solution for scientific analysis and recommend more professional solutions.)
  • All spot, edge and track features can be plotted as specialized graphs, thanks to a dedicated GUI panel.
  • Tracks can be named in TrackScheme. These names are used to sort alphanumerically the tracks as they are laid out. To change the name of a track, just double-click its current name in the TrackScheme view.
  • We use semantic versioning for release numbers from now on. The rules about backward incompatible changes - described below - required a major version change. However, we reserve the right to make a major number change only when there is backward incompatible changes to the user only. API changes might not trigger a major version change.
  • The XML file format changed and is therefore not compatible anymore between major versions. However, XML files generated with the previous version (v1.2) can be imported in v2.0.0. and are converted on the fly.
  • In linear-assignment-problem trackers (LAP tracker and simple LAP tracker), the time interval to bridge gaps is specified in frame interval instead of time interval.
  • In LAP trackers, detection of split and merge events are constrained to two consecutive frames.
  • The spot morphology analyzer is disabled.
  • Removed the spot intensity kurtosis, skewness and variance features.
  • Much better memory management in LAP tracker: Tracking on large number of spots will consume much less memory if tracks are not branching.
  • Speed up considerably the loading of large xml files.
  • Better GUI refreshing when performing heavy calculations.
  • All major operations are now multi-threaded, notably computing spot, edge and track features.
  • Track layout in TrackScheme is now deterministic: when branching, branches are sorted left to right using the name of the first spot in the branches.
  • Spots added manually are added in TrackScheme live in a dedicated column, to facilitate manual tracking.
  • In TrackScheme, added menu items to select tracks downward or upward in time from current selection.
  • In TrackScheme, the selection table can be exported as an ImageJ results table.
  • Better track layout in TrackScheme for tree-like structures.
  • Improved the performance of several track analyzers.
  • Full keyboard navigation.
  • The filter panels that appear in the GUI can have their threshold entered by keyboard: Set the focus to the histogram panel (press tab until the threshold value is displayed in dark red instead of orange, or click the panel), and type a number - possibly decimal, wait 1 s. You can also use the arrow keys to change it by 10% (left/right) or set it to a max or min value (up/down).
  • Fix a nasty and dangerous bug in LoG detector: We were not converting the filter sigma to pixel coordinates, yielding different filter strengths depending on the spatial calibration entered, even if the user-specified radius was the same. This generated a weirdness in spot coordinates that Alison Twelvetrees noted.
  • Fix the bug that caused the GUI to often hang after the initial filtering step.
  • Fix a bug when rendering tracks in the 3D viewer: the filtered-out tracks were displayed anyway. Noticed by David Mason.
  • Fix a bug causing TrackScheme and XML files to sometimes receive empty tracks.
  • Numerous minor bugfixes.

15/03/2013 - v2.0.1

  • Fix a bug noticed by Jan Brocher that prevented track splitting and merging events to be correctly detected in some cases.

22/03/2013 - v2.0.2

  • Fix a bug that prevented selecting edges when the 3D displayer is used.
  • Fix a bug that prevented some spots to be displayed in the side table of TrackScheme.
  • Fix a bug that prevented v2.0.0 xml files to be read.
  • Fix a bug that crashed the 3D viewer when there is no spot in frame.
  • Slight optimization of the 3D viewer startup.

5/6/2013 - v2.0.4

  • Fix a GUI bug, noticed by Tobias Pietzsch.

5/8/2013 - v2.1.0

  • Major rewrite of the core track model to achieve a far better performance when manually editing a very large datasets. You can now interactively edit large datasets without the GUI becoming too sluggish.
  • You can now preview the detection parameters on the current frame before applying it to the whole data.
  • The detection step is now interruptible in the GUI. A click on the cancel button will gracefully interrupt the detection process, and yields the spots found so far. They can be used later on normally.
  • The HyperStack viewer and editor has now a configuration panel that has a log window and some tools for manual annotation.
  • 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 Plugins > Tracking > Load a TrackMate file menu item.
  • There is a new 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 GUI is now resizable.
  • A 'Locale' problem prevented the entering of numerical features correctly on system relying on other decimal separators that the dot. TrackMate now enforces the dot to be used as a decimal separator on all Locales. However there are still reports that this fails on Windows machine with exotic (i.e. non dot as decimal separator) locales.
  • Numerous other bugfixes.