diff --git a/scallops/features/intensity_distribution.py b/scallops/features/intensity_distribution.py index 5d633d4..96c6de0 100644 --- a/scallops/features/intensity_distribution.py +++ b/scallops/features/intensity_distribution.py @@ -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 diff --git a/scallops/features/other.py b/scallops/features/other.py index bd7caaa..adda695 100644 --- a/scallops/features/other.py +++ b/scallops/features/other.py @@ -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 @@ -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] diff --git a/scallops/segmentation/watershed.py b/scallops/segmentation/watershed.py index 4a87f84..1571902 100644 --- a/scallops/segmentation/watershed.py +++ b/scallops/segmentation/watershed.py @@ -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_, )