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TrackMate v7.5.1: new actions to export results and settings persistence.
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@tinevez tinevez released this 17 Jan 13:32
· 327 commits to master since this release
TrackMate-7.5.1
374bd5a

Changes since the v7.1.0

New features.

An action to export a TrackMate session to the Cell-Tracking-Challenge file format.

The cell-tracking challenge website (http://celltrackingchallenge.net/) and paper (https://www.nature.com/articles/nmeth.4473) define a series of metrics on tracking results that help assessing the performance of a tracking pipeline.
This action exports the TrackMate results into a file structure that can be used with the Cell-Tracking Challenge tools.

I acknowledge the great support of the great Vladimir Ulman when building this action.

An action to export the tracking results to a MotilityLab spreadsheet.

MotilityLab is a R application that performs track analysis. It offers many facilities and features that we do not have in TrackMate. One instance is running into a website: http://www.motilitylab.net/startpage.php

There is now an action that facilitates importing TrackMate data into MotilityLab. One of the way to import data into the website is to copy-paste a spreadsheet with specified columns in a given order and format.

This action displays the current tracking results in such a spreadsheet, with the columns pre-formatted, so that it can directly copy-pasted in the website without any extra manipulation.

  • In the TrackMate table: Ctrl+A, Ctrl+C
  • In the MotilityLab import page: Ctrl+V

image

image

An action to export tracking results to Image1 ROIs.

Can be configured to export everything, or just a selection.

image

TrackMate remember parameters between runs.

The parameters used in the GUI are saved and reused the next time you launch TrackMate.
To do this, the settings are saved to a XML file in your home folder, and updated every-time you change panel in the UI.

The file can be found in the .trackmate folder in your home directory, under that name lastusedsettings.xml. It uses the same format that in the TrackMate XML files. It can be safely manually edited. If you run into an issue with weird TrackMate behaviors when launching TrackMate, delete it.

image

<?xml version="1.0" encoding="UTF-8"?>
<TrackMate version="7.5.0">
  <Settings>
    <ImageData filename="TCellsMigration.tif" folder="C:\Users\tinevez\Desktop\TrackMateDLPaper\DemoDatasets\StarDistDetectorCustom\" width="1344" height="1024" nslices="1" nframes="21" pixelwidth="0.6450002483250956" pixelheight="0.6450002483250956" voxeldepth="1.0" timeinterval="1.0" />
    <BasicSettings xstart="0" xend="1343" ystart="0" yend="1023" zstart="0" zend="0" tstart="0" tend="20" />
    <DetectorSettings DETECTOR_NAME="DOG_DETECTOR" TARGET_CHANNEL="1" RADIUS="5.0" THRESHOLD="0.0" DO_MEDIAN_FILTERING="false" DO_SUBPIXEL_LOCALIZATION="true" />
    <InitialSpotFilter feature="QUALITY" value="3.216140548904221" isabove="true" />
    <SpotFilterCollection>
      <Filter feature="QUALITY" value="10.389729536115917" isabove="true" />
    </SpotFilterCollection>

Bugfixes

  • Add a safeguard when saving against badly defined features.
    It is possible to reach the save point with features that have been improperly defined. For instance, a feature might not have declared its isInt flag. This happens for instance when analyzing an image
    with two channels, but forgetting to call the #setNChannels( 2 ) method of the SpotIntensityMultiCAnalyzerFactory.
    This is undesirable but it should not prevent users from saving the data. This commit adds a safeguard that prevents TrackMate from crashing with such features when saving.
  • Fix a bug causing fading tracks in Z not to work if the fading of tracks in time was used.
  • Fix bug in the LoG and DoG detector panels: not abiding to the diameter and threshold shown.
  • Don't crash when trying to save to XML with an unsaved image.
  • Fix directional change edge feature analyzer. Also make the gamma letter used in this feature name appear properly in the results table.
  • Prevent error when the fade track range is out of bounds.
  • Fix remanent ROI in settings.
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