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Add options to segment_3d_image for removing objects touching borders #139

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Merged
ehrenfeu merged 6 commits into from
Apr 7, 2026
Merged

Add options to segment_3d_image for removing objects touching borders #139

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f3f3c8f
Add options to segment_3d_image for removing objects touching borders
Mar 25, 2026
0eab3dd
Refactor segment_3d_image to use RemoveBorderLabelsPlugin for borders…
lguerard Mar 26, 2026
703a7cd
Exclude segment_3d_image from coverage
ehrenfeu Apr 7, 2026
efec83c
Add note about updating dependencies in pyproject.toml
ehrenfeu Apr 7, 2026
032f9ab
Require at least imcf-fiji-mocks 0.14.0
ehrenfeu Apr 7, 2026
f215ea5
Attempt to get coverage for the imports
ehrenfeu Apr 7, 2026
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22 changes: 20 additions & 2 deletions src/imcflibs/imagej/objects3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,15 @@ def imgplus_to_population3d(imp):
return Objects3DPopulation(img)


def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
def segment_3d_image(
imp,
title=None,
min_thresh=1,
min_vol=None,
max_vol=None,
remove_touching_borders=False,
remove_touching_borders_z=False,
):
"""Segment a 3D binary image to get a labelled stack.

Parameters
Expand All @@ -90,6 +98,11 @@ def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
max_vol : int, optional
Maximum volume (in voxels) above which objects get filtered.
Defaults to None.
remove_touching_borders : bool, optional
Whether to remove objects that touch the borders in X and Y. Defaults to False.
remove_touching_borders_z : bool, optional
Comment thread
lguerard marked this conversation as resolved.
Whether to remove objects that touch the z-axis borders. Defaults to False.


Returns
-------
Expand All @@ -107,10 +120,15 @@ def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
labeler.setMinSizeCalibrated(min_vol, img)
if max_vol:
labeler.setMaxSizeCalibrated(max_vol, img)

# Generate labelled segmentation
seg = labeler.getLabels(img)
seg.setScale(cal.pixelWidth, cal.pixelDepth, cal.getUnits())

if remove_touching_borders:
obj = seg.getObjects3DPopulation()
obj.removeObjectsTouchingBorders(seg, remove_touching_borders_z)
seg = ImageHandler.wrap(population3d_to_imgplus(imp, obj))

if title:
seg.setTitle(title)

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