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Jean-Yves Tinevez Profile picture
Jean-Yves Tinevez
@jytinevez
Image analysis, microscopy and software tools for Life Sciences. Facility engineer @ Institut Pasteur
Dec 15, 2022 • 16 tweets • 7 min read
Hello microscopy tweeps.
Do you want to learn the craft of Fluorescence Microscopy *in depth*? Then join us for the @institutpasteur course "Principles and Applications of Fluorescence Microscopy"! In this course, on offer for Masters and PhD students, we intend to teach the optical principles necessary to understand the origin of modern microscopy modalities and resolution, as well as the basics of quantitative image analysis.
Jan 5, 2022 • 20 tweets • 7 min read
Tracking droplets fusion in microfluidic chamber with #TrackMate, a short thread.

Yesterday I got to discuss with Liridon Aliti (on forum.image.sc) about detecting droplet fusion events in movies like this one:

1/ We tried to do it in TrackMate, it was fun and I would like to share how we did it. It serves as a demo of the new TrackMate capabilities, but was done in <10min per movie, so it should not be considered a thorough analysis (we only tried one detector one tracker).

2/
Sep 17, 2021 • 7 tweets • 4 min read
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.
Sep 17, 2021 • 13 tweets • 4 min read
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
Sep 16, 2021 • 29 tweets • 13 min read
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