Merge pull request #27 from HiDiHlabs/dev-clean

sebastiantiesmeyer · web-flow · commit 2454ca00fc1e · 2024-10-22T18:16:11.000+02:00
Dev clean, updated notebook and bug fixes
diff --git a/docs/source/tutorials/xenium_brain.ipynb b/docs/source/tutorials/xenium_brain.ipynb
diff --git a/ovrlpy/_ovrlp.py b/ovrlpy/_ovrlp.py
@@ -1468,7 +1468,7 @@ def run(
 
     print("Running vertical adjustment")
     _assign_xy(df)
-    _assign_z_mean_message_passing(df, rounds=4)
+    _assign_z_mean_message_passing(df, rounds=20)
 
     vis = Visualizer(
         KDE_bandwidth=KDE_bandwidth,
diff --git a/ovrlpy/_utils.py b/ovrlpy/_utils.py
@@ -78,7 +78,10 @@ def _determine_localmax_and_sample(distribution, min_distance=3, min_expression=
 
     """
 
-    rois_x, rois_y = find_local_maxima(distribution, min_distance, min_expression)
+    rois = find_local_maxima(distribution, min_distance, min_expression)
+
+    rois_x = rois[:, 0]
+    rois_y = rois[:, 1]
 
     return rois_x, rois_y, distribution[rois_x, rois_y]
 
