Fix mesh roof height to correctly classify nuclei at all

  Z-slices
  - Changed roof height calculation to use max(mesh_max_z, max_scaled_z) *
  1.05
  - Roof now placed above maximum possible scaled Z coordinate of imaging
  volume
  - Removed Z<27 filters from visualization and analysis scripts
  - Fixes incorrect 'outside' classification for nuclei at Z >= 26

Author: smishra3

EMT_data_analysis/analysis_scripts/Analysis_tools.py

@@ -88,7 +88,6 @@ def load_io_data(df):
     ]]
 
     df_io = io.load_inside_outside_classification()
-    df_io = df_io[df_io['Z']<27]
 
     dfio_merged=pd.merge(df_io, df_info, on='Data ID', suffixes=['','_remove'])
     remove = [col for col in dfio_merged.columns if 'remove' in col]

EMT_data_analysis/analysis_scripts/Nuclei_localization.py

@@ -154,10 +154,22 @@ def localize_for_timepoint(
         v_idx = mesh.find_closest_point(vert)
         mesh.points[v_idx] = new_vert
 
+    # transpose segmentation to XYZ coordinates and set z-scale for isotropic resolution
+    seg = seg.transpose(2, 1, 0)
+    scale = 2.88 / 0.271
+
+    # Calculate roof height to enclose all nuclei in the imaging volume
+    # The roof must be above the maximum possible scaled Z coordinate
+    max_z_slices = seg.shape[2]  # Number of Z slices in imaging volume
+    max_scaled_z = max_z_slices * scale  # Maximum Z after scaling to isotropic
+
     vert, faces = mesh.points, mesh.faces.reshape(mesh.n_faces, 4)[:,1:]
     vert_up = np.zeros_like(vert)
     np.copyto(vert_up, vert)
-    vert_up[:, 2] = max(vert[:,2])*.9
+    # Place roof above the maximum scaled Z coordinate of the imaging volume
+    # This ensures all nuclei (including those at high Z) are enclosed
+    roof_height = max(max(vert[:,2]), max_scaled_z) * 1.05  # 5% margin above max
+    vert_up[:, 2] = roof_height
     face_up = np.zeros_like(faces)
     np.copyto(face_up, faces)
 
@@ -171,10 +183,6 @@ def localize_for_timepoint(
 
     mesh = trimesh.Trimesh(vertices=vw, faces=fw)
 
-    # transpose segmentation to XYZ coordinates and set z-scale for isotropic resolution
-    seg = seg.transpose(2, 1, 0)
-    scale = 2.88 / 0.271
-
     # initialize ray caster (for checking if a point is inside the mesh)
     rayCaster = trimesh.ray.ray_triangle.RayMeshIntersector(mesh)
 

EMT_data_analysis/figure_generation/inside-outside_classification.py

@@ -47,7 +47,6 @@ def main(
     df_meta = df_meta[df_meta['Data ID'] == data_id]
     df = io.load_inside_outside_classification()
     df = df[df['Data ID'] == data_id]
-    df = df[df['Z']<27]
 
     tmp_dir = Path("./emt_tmp/nuclei_localization/")
     tmp_dir.mkdir(exist_ok=True, parents=True)