ultrack CLI documentation clarification

[tischi]

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]

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.