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Update data export scripts #54

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Merged
merged 4 commits into from
Jul 28, 2025
Merged

Update data export scripts #54

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7e77264
Update data export scripts
constantinpape Jul 25, 2025
3b650f7
Update scripts/export_synapse_detections.py
constantinpape Jul 25, 2025
4432c88
Removed relabeling, added ID offset
schilling40 Jul 25, 2025
c267eb3
Warning for data type threshold
schilling40 Jul 28, 2025
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7 changes: 4 additions & 3 deletions scripts/export_lower_resolution.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import zarr

from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
# from skimage.segmentation import relabel_sequential
from skimage.segmentation import relabel_sequential


def filter_component(fs, segmentation, cochlea, seg_name, components):
Expand All @@ -22,7 +22,8 @@ def filter_component(fs, segmentation, cochlea, seg_name, components):
filter_mask = ~np.isin(segmentation, keep_label_ids)
segmentation[filter_mask] = 0

# segmentation, _, _ = relabel_sequential(segmentation)
segmentation, _, _ = relabel_sequential(segmentation)
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@constantinpape constantinpape Jul 25, 2025

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I think that this is the culprit why IHC ids and synapse IDs don't match. We still need to be careful here though, if the max ID exceeds 65,... than we run out of uint16 IDs, which may happen for SGNs and is why I included this.

Maybe the best option is to remove the sequential relabeling here, and to raise a warning if we have larger values than the uint16 max id, as this won't lead to a big issue, just some ID clashes.

segmentation = segmentation.astype("uint16")
return segmentation


Expand All @@ -41,7 +42,7 @@ def export_lower_resolution(args):
s3_store, fs = get_s3_path(internal_path, bucket_name=BUCKET_NAME, service_endpoint=SERVICE_ENDPOINT)
with zarr.open(s3_store, mode="r") as f:
data = f[input_key][:]
print(data.shape)

if args.filter_by_components is not None:
data = filter_component(fs, data, args.cochlea, channel, args.filter_by_components)
if args.binarize:
Expand Down
9 changes: 7 additions & 2 deletions scripts/export_synapse_detections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from tqdm import tqdm


# TODO
def export_synapse_detections(cochlea, scale, output_folder, synapse_name, reference_ihcs, max_dist, radius):
s3 = create_s3_target()

Expand Down Expand Up @@ -53,14 +54,18 @@ def export_synapse_detections(cochlea, scale, output_folder, synapse_name, refer
coordinates /= (2 ** scale)
coordinates = np.round(coordinates, 0).astype("int")

ihc_ids = syn_table["matched_ihc"].values

# Create the output.
output = np.zeros(shape, dtype="uint16")
mask = ball(radius).astype(bool)

for coord in tqdm(coordinates, desc="Writing synapses to volume"):
for coord, matched_ihc in tqdm(
zip(coordinates, ihc_ids), total=len(coordinates), desc="Writing synapses to volume"
):
bb = tuple(slice(c - radius, c + radius + 1) for c in coord)
try:
output[bb][mask] = 1
output[bb][mask] = matched_ihc
except IndexError:
print("Index error for", coord)
continue
Expand Down
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