napari-ctc-io

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 in tiff format, and a corresponding tracklet file *.txt.

• Write tracked cells (labels layer & corresponding tracks 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.