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RegionProperties.intensity_image is deprecated #16

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Merged
joshua-gould merged 2 commits into from
Jan 30, 2026
Merged

RegionProperties.intensity_image is deprecated #16

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2be874c
RegionProperties.intensity_image` is deprecated starting in version 0…
joshua-gould Jan 28, 2026
f3e275b
use intensity_mean
joshua-gould Jan 30, 2026
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2 changes: 1 addition & 1 deletion scallops/features/intensity_distribution.py
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Original file line number Diff line number Diff line change
Expand Up @@ -543,7 +543,7 @@ def _intensity_distribution_old(
/ image_sum
)
frac_pixels_at_d = np.expand_dims(frac_pixels_at_d, 1)
intensity_image = r.intensity_image
intensity_image = r.image_intensity

with np.errstate(divide="ignore", invalid="ignore"):
# Calculate fractional signal intensity per channel
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4 changes: 2 additions & 2 deletions scallops/features/other.py
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Expand Up @@ -30,7 +30,7 @@ def intersects_boundary(
for index in range(len(props)):
r = props[index]
image = r.image.astype(np.uint8)
mask = r.intensity_image[..., channel] * image
mask = r.image_intensity[..., channel] * image
values[index] = np.any(mask != image)
channel_name = channel_names[channel]
result[f"Location_IntersectsBoundary_{channel_name}"] = values
Expand All @@ -55,7 +55,7 @@ def corr_region(
values = np.zeros(len(props))
for index in range(len(props)):
r = props[index]
img_slice = r.intensity_image
img_slice = r.image_intensity
x1 = img_slice[..., c1].flatten()
x2 = img_slice[..., c2].flatten()
corr = np.corrcoef((x1, x2))[1, 0]
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2 changes: 1 addition & 1 deletion scallops/segmentation/watershed.py
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Expand Up @@ -131,7 +131,7 @@ def segment_nuclei_watershed(
labeled = (
_filter_by_region(
labeled,
lambda r: r.mean_intensity,
lambda r: r.intensity_mean,
threshold,
intensity_image=image_,
)
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