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
Got done by the copy / pasting of animated gifs again:
December 10, 2025 at 1:16 PM
Got done by the copy / pasting of animated gifs again:
Erase all labels / selected label
December 10, 2025 at 1:13 PM
Erase all labels / selected label
For instance:
Paint Replace / Add/ Preserve
Paint Replace / Add/ Preserve
December 10, 2025 at 1:13 PM
For instance:
Paint Replace / Add/ Preserve
Paint Replace / Add/ Preserve
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.
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
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.
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.
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.
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
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.
This part has been written with the help of the Claude LLM to help me get the many edge cases right.
Paris 13eme now.
December 1, 2025 at 7:12 AM
Paris 13eme now.
But they are getting fixed. One to go:
November 25, 2025 at 1:42 PM
But they are getting fixed. One to go:
Classical aftermath
November 24, 2025 at 5:26 PM
Classical aftermath
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: