Fix probability map channel reading (#22)

HMS-IDAC · Jun 8, 2023 · cfdf9e1 · cfdf9e1
1 parent 73c7a5e
commit cfdf9e1
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/large/s3seg_qc.py b/large/s3seg_qc.py
@@ -61,7 +61,9 @@ def run_mcmicro(
     channel_names.append('Mask inner outline')
 
     if pmap_path is not None:
-        contour_probability_map = tifffile.imread(pmap_path, key=1)
+        contour_probability_map = (
+            palom.reader.OmePyramidReader(pmap_path).pyramid[0][1].compute()
+        )
         da_contour_probability_map = da.from_array(
             contour_probability_map, chunks=2048
         )