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
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
Reposted by Jean-Yves Tinévez
Reposted by Jean-Yves Tinévez
Reposted by Jean-Yves Tinévez
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
Reposted by Mart Krupovìč, Jean-Yves Tinévez
Reposted by Jean-Yves Tinévez
forum.image.sc/t/bigvolumeb...
Reposted by Jean-Yves Tinévez
Reposted by Jean-Yves Tinévez
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 🤖
forum.image.sc/t/trackmate-...
Enjoy!
And other things.
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
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.
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.
There is a dedicated detector for Cellpose SAM. It takes into account the must lower number of parameters. I have included one: the possibility to pass to the model one channel or all channels. This might impact the segmentation accuracy based on your input.
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
You can now add Spot & track filter parameter sweep in the optimization, to investigate the impact of filtering an tracking accuracy. And the rewrite also yield improved performance and robustness.
In the Helper, you can now optimize tracking parameters with two tracking metrics sets:
- Single Particle Tracking (SPT) challenge metrics for optimizing tracking of moving objects
- And the Cell Tracking Challenge (CTC) metrics Evaluation Methodology
With @lxenard.bsky.social Ko Sugawara, Tobias Pietzsch
GEFF is a new, universal file format for exchanging tracking data between tools. While Java support is still in beta, it’s already used in TrackMate (e.g., for the TrackMate-inTRACKtive integration).