napari-vizsla
Your friendly tracking assistant. Sniff out and fix broken tracks.
There are many fantastic tracking libraries out there (e.g. Trackastra, Ultrack, etc) but in my experience they only get ~90% of tracks right from one frame to the next...over a long movie that's a lot of broken tracks!
napari-vizsla's goal is to help you quickly fix these broken tracks. Load your tracks using the Cell-Tracking-Challenge (CTC) format (which many tracking programs can output) and get fixing!
https://github.com/user-attachments/assets/07aa9885-f69d-4f8c-a1e6-9e69f6b1b936
Usage
napari-vizsla mostly consists of a set of shortcuts to quickly modify and update tracks. It will autosave your changes as you go!
| Keyboard Shortcut | Action |
|---|---|
l |
(l)ink tracks. Select two cells, in two different timepoints, and link them into one track. |
b |
(b)reak track. This breaks the track into two tracklets at the given time point. |
h |
(h)ide overlay. Hides Vizsla overlay. |
t |
hide (t)racks. Hides the track layer. |
s |
hide (s)egmentation layer. Helpful to better see the underlying signal layer. |
Installation
You can install napari-vizsla via pip:
pip install napari-vizsla
If napari is not already installed, you can install napari-vizsla with napari and Qt via:
pip install "napari-vizsla[all]"
Contributing
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
License
Distributed under the terms of the MIT license, "napari-vizsla" is free and open source software
Issues
If you encounter any problems, please [file an issue] along with a detailed description.
1 maintainer
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