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ImageJ ROIs have inscrutable names #1358

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Merged
mrariden merged 4 commits into from
Nov 12, 2025
Merged

ImageJ ROIs have inscrutable names #1358

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87d35ae
added names to ImageJ ROIs
MarinManuel Nov 1, 2025
c5c2224
updated save_rois to ensure labels match mask ids
MarinManuel Nov 11, 2025
f4c8d53
updated save_rois to ensure labels match mask ids
MarinManuel Nov 11, 2025
2d07bd1
Merge branch 'main' of https://github.com/MarinManuel/cellpose4-revMM
MarinManuel Nov 11, 2025
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19 changes: 8 additions & 11 deletions cellpose/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -649,19 +649,16 @@ def save_rois(masks, file_name, multiprocessing=None):
None
"""
outlines = utils.outlines_list(masks, multiprocessing=multiprocessing)
nonempty_outlines = [outline for outline in outlines if len(outline)!=0]
if len(outlines)!=len(nonempty_outlines):
print(f"empty outlines found, saving {len(nonempty_outlines)} ImageJ ROIs to .zip archive.")
rois = [ImagejRoi.frompoints(outline) for outline in nonempty_outlines]
file_name = os.path.splitext(file_name)[0] + '_rois.zip'

rois = []
for i,outline in enumerate(outlines):
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if len(outline) > 0:
rois.append(ImagejRoi.frompoints(outline, name=str(i+1)))

# Delete file if it exists; the roifile lib appends to existing zip files.
# If the user removed a mask it will still be in the zip file
if os.path.exists(file_name):
os.remove(file_name)
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if len(outlines) != len(rois):
print(f"empty outlines found, saving {len(rois)} ImageJ ROIs to .zip archive.")

roiwrite(file_name, rois)
file_name = os.path.splitext(file_name)[0] + '_rois.zip'
roiwrite(file_name, rois, mode='w')


def save_masks(images, masks, flows, file_names, png=True, tif=False, channels=[0, 0],
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