Question about running proseg with cellpose

[EduardGhemes-ICR]

Hi,

I am currently exploring some Xenium data and plan to run proseg starting from cellpose segmentation. At the moment, I do not have access to a GPU, and running cellpose 4 is very time-consuming. As an alternative, I came across turing_segment, which is an optimised version of cellpose, that runs much faster.

I wanted to clarify what input proseg expects when starting analysis from cellpose and if it is possible to use turing_segment instead.

Turing_segment outputs a zarr folder, a metadata file, and polygons.parquet.

Best,
Eduard

[dcjones]

This probably can't be input into proseg directly. Id may be necessary to either convert to a table of transcript assignments or a cell mask file in numpy npy format.

I am working on adding support for reading spatialdata zarr files, but haven't implemented reading cell boundaries. Once I have that done, it should be much easier. Hopefully soon!