New preprint from the IAH facility in @institutpasteur with @guijacquemet lab , @DumenilLab and friends:

Features a new version of #TrackMate, that broadens a lot its versatility.

"Bringing TrackMate in the era of machine-learning and deep-learning"

biorxiv.org/content/10.110…
Link to threads that tries and detail the new stuff:
1/ new detectors and segmentation algorithms based on Deep-Learning and Machine-Learning.
2/ Using TrackMate to segment 3D objects with a slice-by-slice approach.
4/ The announcement post on the Image-SC forum that lists almost all the changes and acknowledge people contributing to this.

forum.image.sc/t/trackmate-v7…
5/ A 70+ manual for the new features, included in the preprint. It includes step-by-step user tutorials and developer documentation for extending TrackMate

biorxiv.org/content/biorxi…
6/ A @ZENODO_ORG collection that contains the data and analysis results used in the tutorials above.

zenodo.org/communities/tr…

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More from @jytinevez

17 Sep
A 2nd post about the new #TrackMate version:
Using TrackMate to segment 3D objects using a slice-by-slice approach.

1/n
Now that we have nice Deep-Learning based and Machine-Learning based segmentation algorithms that work especially well in 2D, we can use them to segment 3D objects with TrackMate.

2/n
The idea is to tell TrackMate "this is not a 3D image but a 2D+T image that you will track".
For instance you could use StarDist on the individual 2D slice to segment sections of the object, then merging the multiple 2D contours in a single 3D object.

3/n
Read 13 tweets
16 Sep
New #TrackMate version out (v&7)
With major changes and improvements I describe below (probably a long thread).

It is the product of a great (and cool) collaboration with @guijacquemet lab (@JwPylvanainen), the @DumenilLab lab in @institutpasteur and the IAH facility

1/n
The new version is the product of an almost Codiv19-induced full rewrite of TrackMate. Our main goal was to allow integrate SOTA segmentation algorithms and tools such as #StarDist, @ilastik_team, #Weka, @MorphoLibJ and #cellpose in TrackMate,

2/n
so that they can be used in a tracking pipeline and improve the tracking accuracy and results.

3/n
Read 29 tweets

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