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royerlab / ultrack

Cell tracking and segmentation software
https://royerlab.github.io/ultrack
BSD 3-Clause "New" or "Revised" License
64 stars 7 forks source link

ultrack CLI documentation clarification #80

Open tischi opened 4 months ago

tischi commented 4 months ago

Hi,

I found this documentation for a CLI interface. However I don't understand how to use it, in particular it often contains the phrase "on napari", which I do not understand.

JoOkuma commented 4 months ago

Hi @tischi,

We use the reader plugins from napari to support multiple file formats, and we index the data using the layer name (or index) they would get in napari viewer. We don't load the napari viewer, so it's safe to use in an HPC.

For example, assuming you have an ome-zarr dataset compatible with the napari-ome-zarr plugin. And your image has three channels: Image, Foreground, and Edges.

So you would use ultrack segment --cfg config.toml -r napari-ome-zarr -dl Foreground -el Edges To indicate it should use the napari-ome-zarr to open your dataset and the detection and edges channels are respectively Foreground and Edges.