[BUG] Project-wise cell segmentation does not run

[Sbrussee]

Description

When trying to apply cell segmentation on a newly constructed project, the segmentation does not seem to run at all. The slides were loaded properly, as shown by the log output:

INFO Segmenting cells for 717 slides.

However, after this step, i see no increase in memory or cpu usage or gpu usage for hours, suggesting the segmentation itself does not properly start. I checked the tile_um the cell segmentation function produced and it is 512, which seems normal. Increasing the number of workers or changing the window_size did not have any effect. Is there maybe another function i should call first before using cell_segmentation? Thanks a lot for your help!

To Reproduce

Code to reproduce the behaviour: project.cell_segmentation(diam_um=30, qc='Otsu', verbose=True, tile=True, batch_size=16, model='cyto2', mpp=0.25, window_size=512, num_workers=1, sources=['MyProject'])

Environment:

• Slideflow Version (e.g., 1.0): 2.3.0
• OS (e.g., Ubuntu): Rocky Linux 8.9
• How you installed Slideflow (pip, source): using pip
• Python version: 3.9.17
• CUDA/cuDNN version: 11.6.1
• GPU models and configuration: Quadro RTX 6000
• Any other relevant information: Cellpose seems to be installed properly

[Sbrussee]

Closing this, turns out my MPP was not read properly (using .tiff files) which silently made slide not work.