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
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
Optimistic Dominik
November 24, 2025 at 10:50 AM
Optimistic Dominik
With an image with a proper background >.<
November 20, 2025 at 2:46 PM
With an image with a proper background >.<
We have made an example use of YOLO to track bacteria against a complex background, to be released soonish.
November 20, 2025 at 11:42 AM
We have made an example use of YOLO to track bacteria against a complex background, to be released soonish.
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.
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.
November 20, 2025 at 11:42 AM
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.
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.
- new Cellpose 3 integration
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
November 20, 2025 at 11:42 AM
- new Cellpose 3 integration
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Reworked the Cellpose integration, and add Omnipose and Cellpose-SAM
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
November 20, 2025 at 11:42 AM
Reworked the Cellpose integration, and add Omnipose and Cellpose-SAM
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
The Segmentation Editor
TrackMate now includes a 2D segmentation editor based on LabKit, allowing users to create and manually edit object shapes in 2D. With the track edition capabilities of TrackMate, it makes it possible to generate 2D tracking ground truth from scratch in an efficient manner.
TrackMate now includes a 2D segmentation editor based on LabKit, allowing users to create and manually edit object shapes in 2D. With the track edition capabilities of TrackMate, it makes it possible to generate 2D tracking ground truth from scratch in an efficient manner.
November 20, 2025 at 11:42 AM
The Segmentation Editor
TrackMate now includes a 2D segmentation editor based on LabKit, allowing users to create and manually edit object shapes in 2D. With the track edition capabilities of TrackMate, it makes it possible to generate 2D tracking ground truth from scratch in an efficient manner.
TrackMate now includes a 2D segmentation editor based on LabKit, allowing users to create and manually edit object shapes in 2D. With the track edition capabilities of TrackMate, it makes it possible to generate 2D tracking ground truth from scratch in an efficient manner.
Mainly, we introduce a novel spot segmentation editor, that allows you to edit the shape of objects in 2D. And we have created a new framework to integrate Python algorithms (among others) and use it to considerably increase the number of tools at your fingertips in TrackMate:
November 20, 2025 at 11:42 AM
Mainly, we introduce a novel spot segmentation editor, that allows you to edit the shape of objects in 2D. And we have created a new framework to integrate Python algorithms (among others) and use it to considerably increase the number of tools at your fingertips in TrackMate:
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Scientific fois gras is on the way
November 16, 2025 at 2:55 PM
Scientific fois gras is on the way
Copenhagen I am in you!
November 10, 2025 at 9:50 PM
Copenhagen I am in you!
When in Rome, do as the Romans do
Go teams!
Go teams!
November 2, 2025 at 2:40 AM
When in Rome, do as the Romans do
Go teams!
Go teams!
Some analysts understood all about life
September 18, 2025 at 3:54 PM
Some analysts understood all about life
I will speak about the course again, but if you feel like meeting and learning bioimage analysis, mark your calendar and let's' meet in June in beautiful Paris
September 10, 2025 at 12:50 PM
I will speak about the course again, but if you feel like meeting and learning bioimage analysis, mark your calendar and let's' meet in June in beautiful Paris
I cannot resist posting pictures of the 2025 edition:
September 10, 2025 at 12:50 PM
I cannot resist posting pictures of the 2025 edition:
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
September 10, 2025 at 12:50 PM
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
Post a non-religious photo you think of holy.
August 21, 2025 at 6:31 AM
Post a non-religious photo you think of holy.