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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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Extracted cropped spot images #820

Open KSimi7 opened 2 months ago

KSimi7 commented 2 months ago

Hi!

Thank you for developing this package. Is there any way I can export the cropped spot images as a numpy arrays or individual images? I look forward to hearing from you!

giovp commented 2 months ago

hi, thank youf ro your interest in squidpy, what do you mean "export the cropped spot as numpy arrays"? with the function generate_spot_crops you should be able to do just that, as it returns a generator with cropped tiles at the centroid coordinates of the visium array.