diff --git a/spatiomic/segment/_assign_communities.py b/spatiomic/segment/_assign_communities.py index 727ea78..75ef4e7 100644 --- a/spatiomic/segment/_assign_communities.py +++ b/spatiomic/segment/_assign_communities.py @@ -50,8 +50,9 @@ def assign_communities( # Initialize output with same shape as masks community_image = np.zeros_like(masks) - # Assign community labels (adding 1 to avoid confusion with background) + # Assign community labels (adding 1 to avoid confusion with background, if needed) + pseudocount = 1 if communities_array.min() == 0 else 0 for i, region_id in enumerate(unique_regions): - community_image[masks == region_id] = communities_array[i] + 1 + community_image[masks == region_id] = communities_array[i] + pseudocount return community_image