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Add x,y coords and cell size in pixels to Nimbus final results #58

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Merged
JLrumberger merged 2 commits into from
Apr 21, 2026
Merged

Add x,y coords and cell size in pixels to Nimbus final results #58

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22f9ea2
Add centroid x,y coords and cell area to Nimbus final results
Copilot Apr 17, 2026
ece5dfc
Add clarifying comments for centroid axis mapping
Copilot Apr 17, 2026
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5 changes: 4 additions & 1 deletion src/nimbus_inference/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -551,7 +551,7 @@ def segment_mean(instance_mask, prediction):
"""
props_df = regionprops_table(
label_image=instance_mask.astype(np.int32), intensity_image=prediction,
properties=['label' , 'centroid', 'intensity_mean']
properties=['label' , 'centroid', 'area', 'intensity_mean']
)
return props_df

Expand Down Expand Up @@ -663,6 +663,9 @@ def predict_fovs(
if df_fov.empty:
df_fov["label"] = df["label"]
df_fov["fov"] = os.path.basename(fov_path)
df_fov["centroid_x"] = df["centroid-1"] # column dimension
df_fov["centroid_y"] = df["centroid-0"] # row dimension
df_fov["area"] = df["area"]
df_fov[channel_name] = df["intensity_mean"]
if save_predictions:
os.makedirs(out_fov_path, exist_ok=True)
Expand Down
4 changes: 2 additions & 2 deletions tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -300,7 +300,7 @@ def segmentation_naming_convention(fov_path):
assert len(cell_table) == 15
# check if we get the correct columns (fov, label, CD4, CD56)
assert np.alltrue(
set(cell_table.columns) == set(["fov", "label", "CD4", "CD56"])
set(cell_table.columns) == set(["fov", "label", "centroid_x", "centroid_y", "area", "CD4", "CD56"])
)
# check if predictions don't get written to output_dir
assert not os.path.exists(os.path.join(output_dir, "fov_0", "CD4.tiff"))
Expand Down Expand Up @@ -332,7 +332,7 @@ def segmentation_naming_convention(fov_path):
assert len(cell_table) == 15
# check if we get the correct columns (fov, label, CD4, CD56)
assert np.alltrue(
set(cell_table.columns) == set(["fov", "label", "CD4", "CD56"])
set(cell_table.columns) == set(["fov", "label", "centroid_x", "centroid_y", "area", "CD4", "CD56"])
)


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