added elf wrapper to cristae segment function #162
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…eground prediction. Added binary erosion to mito_seg to avoid detecting cristae between mitochondria
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@constantinpape the changes we discussed are implemented now |
| mito_seg=None, | ||
| erode_voxels=3, | ||
| ): | ||
| if mito_seg is not None: |
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This will not be None given the current logic. I would avoid this check and directly apply the postprocessing.
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| # get the segmentation via seeded watershed | ||
| # Process instance erosion using global regionprops | ||
| if erode_voxels > 0: |
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I would refactor this into a small function to improve the code readability.
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| # Load into memory to get accurate global bounding boxes and sizes. | ||
| # this can cause issue with limited memory (RAM) | ||
| mito_data = mito_seg[:] if hasattr(mito_seg, '__getitem__') else mito_seg |
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In which case would we not have a __getitem__?
| # Load into memory to get accurate global bounding boxes and sizes. | ||
| # this can cause issue with limited memory (RAM) | ||
| mito_data = mito_seg[:] if hasattr(mito_seg, '__getitem__') else mito_seg | ||
| eroded_mito_data = np.zeros_like(mito_data) |
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You can do this in-place, i.e. directly write the output to mito_data. Then you avoid allocating the memory twice.
| t0 = time.time() | ||
| ids, sizes = parallel.unique(seg, return_counts=True, block_shape=block_shape, verbose=verbose) | ||
| filter_ids = ids[sizes < min_size] | ||
| seg[np.isin(seg, filter_ids)] = 0 |
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np.isin is very memory hungry. There is an implementation in elf.parallel you could use instead if you want to save memory.
… be more memory efficient
constantinpape
approved these changes
Mar 20, 2026
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and also masked the foreground prediction. Added binary erosion to mito_seg to avoid detecting cristae between mitochondria.
This resolves following issues: