Segm m cellpose #9
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LouisK92
requested changes
Nov 22, 2024
LouisK92
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Nov 22, 2024
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Here I added Cellpose method into the cellpose component.
Cellpose is imported from txsim.
as an input for the method itself I give
image = sdata['morphology_mip']['scale0'].image.compute().to_numpy()
transformation = sdata['morphology_mip']['scale0'].image.transform.copy()
img_arr = tx.preprocessing.segment_cellpose(image[0], hyperparameters)
as far as you mentioned that we will switch to another input format: it would not be zarr file with iteration across all scales and images, but the cropped image itself. As far as in the pipeline it's still missing, I added it's like that
All test successfully passed
