napari-ctc-io
-
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.
1 maintainer
Metadata
1 maintainer
Release files for napari-ctc-io 0.2.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| napari_ctc_io-0.2.1.tar.gz | 1.4 MB | Without provenance | Details for napari_ctc_io-0.2.1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
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| napari_ctc_io-0.2.1-py3-none-any.whl | Python 3 | none | any | Details for napari_ctc_io-0.2.1-py3-none-any.whl |
Total release size: 2.8 MB
Release files / napari_ctc_io-0.2.1.tar.gz
| Download URL | napari_ctc_io-0.2.1.tar.gz |
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| Size | 1.4 MB |
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| Download URL | napari_ctc_io-0.2.1-py3-none-any.whl |
|---|---|
| Size | 1.4 MB |
| Tags | Python 3 |
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