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Fix export of touching objects to IMOD #155

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Merged
constantinpape merged 2 commits into from
Feb 4, 2026
Merged

Fix export of touching objects to IMOD #155

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d15427d
Separate touching instances before export to IMOD
constantinpape Feb 4, 2026
4ede513
Bump version
constantinpape Feb 4, 2026
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2 changes: 1 addition & 1 deletion synapse_net/__version__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.4.0"
__version__ = "0.4.1"
20 changes: 16 additions & 4 deletions synapse_net/imod/to_imod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import numpy as np
from scipy.ndimage import distance_transform_edt
from skimage.measure import regionprops
from skimage.segmentation import find_boundaries
from tqdm import tqdm


Expand All @@ -27,6 +28,14 @@ def _load_segmentation(segmentation_path, segmentation_key):
return seg


def _separate_instances(segmentation):
boundaries = find_boundaries(segmentation, mode="outer")
boundaries &= (segmentation != 0)
segmentation = segmentation.copy()
segmentation[boundaries] = 0
return segmentation


# TODO: this has still some issues with some tomograms that has an offset info.
# For now, this occurs for the inner ear data tomograms; it works for Fidi's STEM tomograms.
# Ben's theory is that this might be due to data form JEOL vs. ThermoFischer microscopes.
Expand All @@ -37,6 +46,7 @@ def write_segmentation_to_imod(
segmentation: Union[str, np.ndarray],
output_path: str,
segmentation_key: Optional[str] = None,
separate_instances: bool = True,
) -> None:
"""Write a segmentation to a mod file as closed contour object(s).

Expand All @@ -45,6 +55,7 @@ def write_segmentation_to_imod(
segmentation: The segmentation (either as numpy array or filepath to a .tif file).
output_path: The output path where the mod file will be saved.
segmentation_key: The key to the segmentation data in case the segmentation is stored in hdf5 files.
separate_instances: Whether to seperate touching instances before the export.
"""
cmd = "imodauto"
cmd_path = shutil.which(cmd)
Expand All @@ -55,6 +66,8 @@ def write_segmentation_to_imod(
segmentation = _load_segmentation(segmentation, segmentation_key)

# Binarize the segmentation and flip its axes to match the IMOD axis convention.
if separate_instances:
segmentation = _separate_instances(segmentation)
segmentation = (segmentation > 0).astype("uint8")
segmentation = np.flip(segmentation, axis=1)

Expand Down Expand Up @@ -209,13 +222,13 @@ def _pad(inp, n=3):
x = _pad(coord[2])
y = _pad(shape[1] - coord[1])
z = _pad(coord[0])

else:
# (y, x) indexing, single z-plane
x = _pad(coord[1])
y = _pad(shape[0] - coord[0])
z=_pad(0)
z = _pad(0)

f.write(f"{x}{y}{z}{_pad(radius, 2)}\n")
cmd = [cmd, "-si", "-scat", fname, output_path]

Expand All @@ -227,7 +240,6 @@ def _pad(inp, n=3):
run(cmd)



def write_segmentation_to_imod_as_points(
mrc_path: str,
segmentation: Union[str, np.ndarray],
Expand Down