Drag and drop annotations/results in the Cell Tracking Challenge (CTC) format into napari.
Project description
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 intiff
format, and a corresponding tracklet file*.txt
. -
Write tracked cells (
labels
layer & correspondingtracks
layer) 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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for napari_ctc_io-0.2.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d70907dab04a01060d86096d2ac5626b6d1069524eb8b165d800767587c0545f |
|
MD5 | 762baf7255471ad1099bb37fb876c341 |
|
BLAKE2b-256 | 28d18c7655187203f33f01e12ca3a142568a600263671736c403203355b79fc4 |