Postprocess ihc #33
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Postprocess ihc #33
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constantinpape
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The current adaptation splits the functions into SGN and IHC. They can probably be more generalized, but this circumvents the adaptation of the prior erosion before using the connected graph components.
Splitting this makes sense. We can discuss more adaptations next week.
| def run_unet_segmentation_slurm( | ||
| output_folder: str, | ||
| min_size: int, | ||
| boundary_distance_threshold: float = 0.5, |
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We should also expose the center_distance_threshold here.
scripts/extract_block.py
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| with zarr.open(s3_path, mode="r") as f: | ||
| raw = f[input_key][roi] | ||
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| elif ".tif" in input_path: |
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I would change this to if input_key is None. That's more consistent to how we handle this otherwise in the codebase.
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| # create edges between points whose distance is less than threshold min_edge_distance | ||
| for i in coords: | ||
| for j in coords: |
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This looks wrong. Shouldn't i, j be indices into the respective array or list?
So
for i in range(len(coords))
etc. ?
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Adapt post-processing for the segmentation of inner hair cells (IHCs).
The current adaptation splits the functions into SGN and IHC. They can probably be more generalized, but this circumvents the adaptation of the prior erosion before using the connected graph components.
WIP