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Image processing with stardist #11

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alipirani88 opened this issue Nov 12, 2024 · 0 comments
Open

Image processing with stardist #11

alipirani88 opened this issue Nov 12, 2024 · 0 comments
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@alipirani88
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Hi, I am ex=ncountering this error while stardist image processing. Any idea what might be causing this error?

Traceback (most recent call last):
File "/rsrch5/home/neuro_rsrch/apirani/2024_11_07_Enact_Demo/enact_915422.py", line 9, in
so_hd.run_enact()
File "/home/apirani/.local/lib/python3.10/site-packages/enact/pipeline.py", line 999, in run_enact
cell_labels, cell_polys = self.segment_cells(image=wsi_norm)
File "/home/apirani/.local/lib/python3.10/site-packages/enact/pipeline.py", line 318, in segment_cells
labels, polys = self.stardist_model.predict_instances_big(
File "/home/apirani/.local/lib/python3.10/site-packages/stardist/models/base.py", line 930, in predict_instances_big
blocks = BlockND.cover(img.shape, axes, block_size, min_overlap, context, grid)
File "/home/apirani/.local/lib/python3.10/site-packages/stardist/big.py", line 448, in cover
cover_1d = [Block.cover(*args) for args in zip(shape, block_size, min_overlap, context, grid)]
File "/home/apirani/.local/lib/python3.10/site-packages/stardist/big.py", line 448, in
cover_1d = [Block.cover(args) for args in zip(shape, block_size, min_overlap, context, grid)]
File "/home/apirani/.local/lib/python3.10/site-packages/stardist/big.py", line 186, in cover
assert 0 <= min_overlap+2
context < block_size <= size
AssertionError

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