Jean-Yves Tinevez
LightNews LightNews
banner
jytinevez.bsky.social
Jean-Yves Tinevez
@jytinevez.bsky.social
2.1K followers 680 following 280 posts

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 .. more

Videos
Biology 51%
Engineering 10%
Posts Replies Media Videos

Reposted by Jean-Yves Tinévez, Olivier Sandre

amichaut.bsky.social
Arthur Michaut 🔬🐣 @amichaut.bsky.social · 1d
🚨 Je cherche des chercheur-ses de toutes disciplines pour un doc radio pour parler de leur sujet de recherche mais aussi de leur quotidien (une journée type au labo). Contrainte supplémentaire, le labo doit être hors de Paris.
Plus d'infos : forms.gle/hw9wH2p5UH4A...
Interview de chercheur-ses pour doc radio
À l'occasion d'un projet de documentaire radio sur France Culture, je cherche des chercheur-ses représentant une diversité de disciplines mais également de statuts à interviewer. L'idée est de partir...
forms.gle

Reposted by Jean-Yves Tinévez

pasteur.fr
Institut Pasteur | 130 years of biomedical research @pasteur.fr · 4d
🏆 4 Institut Pasteur scientists awarded by French Academy of Sciences @academiesciences.bsky.social

🥇 Romain Levayer
🥇 Pierre-Jean Corringer
🥇 Eduardo Rocha
🥇 Hervé Bourhy

Congratulations !
4 Institut Pasteur scientists awarded by French Academy of Sciences

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 6d
Paris 13eme now.

Reposted by Jean-Yves Tinévez

gfrasca.bsky.social
Guillaume Frasca @gfrasca.bsky.social · 9d
Participez à l'étude #POPCORN lancée par l'équipe "Épidémiologie des maladies émergentes" de l'Institut @pasteur.fr pour comprendre l’évolution des attitudes et des comportements à l’égard des mesures préventives si nous devions faire face à une nouvelle #pandémie redcap.link/popcorn-past...
a man in a striped sweater is sitting on a couch
ALT: a man in a striped sweater is sitting on a couch
media.tenor.com

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 10d
This looks great! OrganoidTracker 2.0 performs tracking AND returns estimate of the tracking error rate **locally**.
Interesting for frameworks that guide users towards plausible tracking mistakes

www.nature.com/articles/s41...
Cell tracking with accurate error prediction - Nature Methods
OrganoidTracker 2.0 enables fast and accurate cell tracking in complex systems such as developing organoids. A key aspect of the work is determining cell tracks with error probabilities for any tracki...
www.nature.com

Reposted by Jean-Yves Tinévez

guijacquemet.bsky.social
Guillaume Jacquemet @guijacquemet.bsky.social · 10d
Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out

Customizable FDM-based zebrafish embryo mold for live imaging
www.biorxiv.org/content/10.1...

Work by Marcela and Jaakko in the lab

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 11d
Eurostar: it’s a train but you’ll be as miserable as in an airport

Reposted by Jean-Yves Tinévez

cbias.bsky.social
Crick BioImage Analysis Symposium @cbias.bsky.social · 11d
Second speaker is @jytinevez.bsky.social from @institutpasteur.bsky.social introducing TrackMate 8 #CBIAS2025

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 11d
But they are getting fixed. One to go:

Reposted by Jean-Yves Tinévez

david-j-barry.bsky.social
Dave Barry @david-j-barry.bsky.social · 11d
BIOIMAGE ANALYSTS ASSEMBLE!!!

#CBIAS2025

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 12d
Classical aftermath

Reposted by Jean-Yves Tinévez

pasteuredu.bsky.social
Institut Pasteur Education @pasteuredu.bsky.social · 12d
🎥 Discover the Institut Pasteur Education Center!

We’re excited to unveil the new presentation video of our Education Center, a space dedicated to training the next generation of scientists, health professionals, and researchers from around the world

➡️ www.pasteur.fr/en/education...

@pasteur.fr
Discover the Education Center of the Institut Pasteur
YouTube video by Institut Pasteur EDUCATION
youtu.be

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 13d
Optimistic Dominik

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 13d
My bad, it's actually #CBIAS2025

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 13d
#CBIAS 2025 let’s go!!

Reposted by Mart Krupovìč, Jean-Yves Tinévez

chzimmer.bsky.social
Christophe Zimmer @chzimmer.bsky.social · 13d
Recently out: “Uniform dynamics of cohesin-mediated loop extrusion in living human cells”. In this study led by brilliant former PhD student Thomas Sabaté we use live cell microscopy and polymer simulations to characterize how DNA loops and TADs form in human cells by cohesin-driven extrusion. (1/4)

Reposted by Jean-Yves Tinévez

ekatrukha.bsky.social
Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 16d
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc

Reposted by Jean-Yves Tinévez

bengallusser.bsky.social
Ben Gallusser @bengallusser.bsky.social · 16d
Give it a try following the tutorial made by @jytinevez.bsky.social imagej.net/plugins/trac...
TrackMate Trackastra
Trackastra integration in TrackMate.
imagej.net

Reposted by Jean-Yves Tinévez

bengallusser.bsky.social
Ben Gallusser @bengallusser.bsky.social · 16d
Trackastra is part of the brand-new TrackMate v8.

It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.

Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 16d
With an image with a proper background >.<

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
More details and images that are not @#$23-up here:
forum.image.sc/t/trackmate-...
TrackMate v8 - segmentation editor and Python CLI integration
TrackMate v8: 2D Segmentation Editor & Python CLI Integration Hi everyone, I am excited to announce TrackMate v8, a major update introducing key improvements for both end-users and developers. Mai...
forum.image.sc

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
We hope you will enjoy this new version which took us a lot of time and sweat. I am confident that the new integration will accelerate bringing SOTA segmentation and linking algorithms into a convenient platform.

Enjoy!

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
I will be in the #CBIAS conference next week, in the Crick London. I will be happy to discuss the new version in person. Come and say hi!

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
And I improved a bit the display of column headers in TrackScheme. No big deal.

And other things.

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
There was also an annoying bug with 3D detection giving off coordinates, that was discussed reported and discussed here several times:

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
Other Improvements & Bug Fixes:

The most important bugfix we introduce is the memory leak that was evading us for a long time. To fix it I completely redesigned the detector factory API, introducing big breaking changes

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
We have made an example use of YOLO to track bacteria against a complex background, to be released soonish.

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
YOLO integration

With Marie Anselmet. Here we integrated the object detection routine of YOLO, so objects are detected as boxes and add in TrackMate as circular spots. YOLO does not ship pretrained model for microscopy, so you will have to provide or train one yourself.

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
Trackastra integration

With Martin Weigert & Benjamin Galluser: Integrated Trackastra as a tracker into TrackMate. This required some changes in Trackastra CLI and a rework of the tracker API of TrackMate.

jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · 17d
Spotiflow integration

With @albertdm.bsky.social - Spotiflow can now be run directly from TrackMate!