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added seed_distance to parameters of mitochondria segmentation #93

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merged 4 commits into from
Jan 9, 2025
Merged

added seed_distance to parameters of mitochondria segmentation #93

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32438b2
added seed_distance to parameters of mitochondria segmentation
lufre1 Jan 8, 2025
583781e
added blockshape and halo for seeded watershed as well and removed ob…
lufre1 Jan 9, 2025
3e62c91
Apply suggestions from code review
constantinpape Jan 9, 2025
6c74bd7
Update environment.yaml
constantinpape Jan 9, 2025
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7 changes: 4 additions & 3 deletions synapse_net/inference/mitochondria.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ def _run_segmentation(
foreground, boundaries, verbose, min_size,
# blocking shapes for parallel computation
block_shape=(128, 256, 256),
halo=(48, 48, 48)
halo=(48, 48, 48),
seed_distance=6
):
t0 = time.time()
boundary_threshold = 0.25
Expand All @@ -24,7 +25,6 @@ def _run_segmentation(

# Get the segmentation via seeded watershed.
t0 = time.time()
seed_distance = 6
seeds = np.logical_and(foreground > 0.5, dist > seed_distance)
seeds = parallel.label(seeds, block_shape=block_shape, verbose=verbose)
if verbose:
Expand Down Expand Up @@ -65,6 +65,7 @@ def segment_mitochondria(
return_predictions: bool = False,
scale: Optional[List[float]] = None,
mask: Optional[np.ndarray] = None,
seed_distance: int = 6,
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You should add this to the doc string as well.

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i added watershed tiling to the function's parameters, because i needed to adapt it for some data

) -> Union[np.ndarray, Tuple[np.ndarray, np.ndarray]]:
"""Segment mitochondria in an input volume.

Expand Down Expand Up @@ -97,7 +98,7 @@ def segment_mitochondria(

# Run segmentation and rescale the result if necessary.
foreground, boundaries = pred[:2]
seg = _run_segmentation(foreground, boundaries, verbose=verbose, min_size=min_size)
seg = _run_segmentation(foreground, boundaries, verbose=verbose, min_size=min_size, seed_distance=seed_distance)
seg = scaler.rescale_output(seg, is_segmentation=True)

if return_predictions:
Expand Down
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