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Add options to segment_3d_image for removing objects touching borders #139

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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
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30 changes: 27 additions & 3 deletions src/imcflibs/imagej/objects3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from de.mpicbg.scf.imgtools.image.create.image import ImageCreationUtilities
from de.mpicbg.scf.imgtools.image.create.labelmap import WatershedLabeling
from ij import IJ
from inra.ijpb.plugins import RemoveBorderLabelsPlugin
from mcib3d.geom import Objects3DPopulation
from mcib3d.image3d import ImageHandler, ImageLabeller
from mcib3d.image3d.processing import MaximaFinder
Expand Down Expand Up @@ -71,7 +72,15 @@ 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 +99,11 @@ 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
Whether to remove objects that touch the z-axis borders. Defaults to False.


Returns
-------
Expand All @@ -107,14 +121,24 @@ 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())

seg = RemoveBorderLabelsPlugin().remove(
seg.getImagePlus(),
remove_touching_borders,
remove_touching_borders,
remove_touching_borders,
remove_touching_borders,
remove_touching_borders_z,
remove_touching_borders_z,
)

if title:
seg.setTitle(title)

return seg.getImagePlus()
return seg


def maxima_finder_3d(imp, min_threshold=0, noise=100, rxy=1.5, rz=1.5):
Expand Down
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