Read CTC format
Drag and drop/write tracks from/to the Cell Tracking Challenge (CTC) format.
-
Drag and drop annotations/results in the Cell Tracking Challenge (CTC) format into napari.
Works for
TRA,RES, etc. folders, which contain a time sequence of segmentations intiffformat, and a corresponding tracklet file*.txt. -
Write tracked cells (
labelslayer & correspondingtrackslayer) to CTC format (see usage below).
https://github.com/bentaculum/napari-ctc-io/assets/8866751/197c9ea2-4115-4829-851a-4b77eb843bf2
Installation
You can install napari-ctc-io via pip:
pip install napari-ctc-io
To install latest development version :
pip install git+https://github.com/bentaculum/napari-ctc-io.git
Usage of writer in widget
def _save(self, event=None):
pm = npe2.PluginManager.instance()
outdir = "TRA"
writer_contrib = pm.get_writer(
outdir,
["labels", "tracks"],
"napari-ctc-io",
)[0]
save_layers(
path=outdir,
layers=[
self._viewer.layers["masks_tracked"],
self._viewer.layers["tracks"],
],
plugin="napari-ctc-io",
_writer=writer_contrib,
)
Contributing
Contributions are very welcome. Tests can be run with tox.
License
Distributed under the terms of the BSD-3 license,
napari-ctc-io is free and open source software.
Issues
If you encounter any problems, please file an issue along with a detailed description.
Version:
- 0.2.1
Last updated:
- 2024-11-13
First released:
- 2024-06-04
License:
- BSD-3-Clause
Supported data:
- Information not submitted
Plugin type:
Save extension: