Jean-Yves Tinevez
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jytinevez.bsky.social
Jean-Yves Tinevez
@jytinevez.bsky.social
Research engineer and core facility manager at the Institut Pasteur
https://research.pasteur.fr/en/team/image-analysis-hub/
Everything #TrackMate #Mastodon-sc (the tool to track lineages in microscopy videos, not the social networks etc).
Views are my own
Yep exactly.
SAMJ is based on the preview off a brand new technology called appose that does everything transparently (download etc)
TrackMate 9 will be based on that

Summoning @ctrue.bsky.social
December 10, 2025 at 6:51 PM
December 10, 2025 at 1:16 PM
December 10, 2025 at 1:16 PM
December 10, 2025 at 1:16 PM
December 10, 2025 at 1:16 PM
Got done by the copy / pasting of animated gifs again:
December 10, 2025 at 1:16 PM
I am very grateful to my colleagues in the F-BIAS team that helped me find and address edge cases for the conda autodetection.

Enjoy!
December 10, 2025 at 1:13 PM
etc. They are described and documented here:
imagej.net/plugins/trac...
Editing object shape in TrackMate
Tutorial on how to use TrackMate segmentation editor to modify object shape.
imagej.net
December 10, 2025 at 1:13 PM
Erase all labels / selected label
December 10, 2025 at 1:13 PM
For instance:

Paint Replace / Add/ Preserve
December 10, 2025 at 1:13 PM
New editing modes for the TrackMate segmentation editor

In the v8.1 we introduce editing modes for the segmentation editor of TrackMate. These modes leverage the capabilities of Labkit to facilitate the edition of segmentation masks.
December 10, 2025 at 1:13 PM
Second, there is a better TrackMate conda configuration tool, that tries to autodetect where conda is installed on users system, and try to input sensible values in the configuration plugin.

This part has been written with the help of the Claude LLM to help me get the many edge cases right.
December 10, 2025 at 1:13 PM
First, Python tools are now ran using conda run everywhere. This should fix most of the “0 spots found” bug we see occuring.
December 10, 2025 at 1:13 PM
Additionally, the way we run Python tools installed in conda environment is still too brittle, relying on conda activate or inferred path to python executables. This new version aims at making all of this more robust and easy to use.
December 10, 2025 at 1:13 PM
First, we reworked the conda configuration and the way conda tools are run in TrackMate.

It seems that there are almost as many conda installations as users in biology, and the difficulty of finding where conda is installed and what to input proves to be a hurdle to many TrackMate users.
December 10, 2025 at 1:13 PM