update

wanglab-broad · Oct 11, 2021 · e1d1bf5 · e1d1bf5
1 parent ae45ec2
commit e1d1bf5
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Showing 7 changed files with 1,477 additions and 16 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/ClusterMap/clustermap.py b/ClusterMap/clustermap.py
@@ -68,6 +68,7 @@ def segmentation(self,cell_num_threshold=0.015, dapi_grid_interval=5, add_dapi=T
             print('DPC')
             cell_ids = DPC(self,all_coord, all_ngc,cell_num_threshold,use_genedis)
         else:
+            self.num_spots_with_dapi=0
             spatial = np.array(spots_denoised[['spot_location_1', 'spot_location_2', 'spot_location_3']]).astype(np.float32)
             print('DPC')
             cell_ids = DPC(self,spatial,ngc, cell_num_threshold, use_genedis)
@@ -82,7 +83,7 @@ def segmentation(self,cell_num_threshold=0.015, dapi_grid_interval=5, add_dapi=T
 
         print('Postprocessing')
         erase_small_clusters(self.spots,self.min_spot_per_cell)
-#         res_over_dapi_erosion(self.spots, self.dapi_binary)
+        res_over_dapi_erosion(self.spots, self.dapi_binary)
 
         # Keep all spots id for plotting
         is_remain=np.in1d(cell_ids, self.spots['clustermap'].unique())

diff --git a/ClusterMap/postprocessing.py b/ClusterMap/postprocessing.py
@@ -17,7 +17,7 @@ def res_over_dapi_erosion(spots, dapi_binary, method='clustermap', minus1 = Fals
     returns :   None
     '''
 
-    dapi_binary_eroded = erosion(dapi_binary, ball(2))
+    dapi_binary_eroded = dapi_binary
     cell_list = np.unique(spots[method])[1:]
     if minus1:
         for cell in cell_list:

diff --git a/ClusterMap/utils.py b/ClusterMap/utils.py
@@ -203,11 +203,14 @@ def DPC(self,all_coord, all_ngc, cell_num_threshold, spearman_metric=spearman_me
     list12not=[not x for x in list12]
     self.cellcenter=all_coord[list12,:]
 
-    print(f'  Find cell number:{number_cell}')
+
 
 
     #assign the remaining spots
     cellid=np.zeros((self.num_spots_with_dapi,))-1
+    self.number_cell=sum(list12)
+    print(f'  Find cell number:{number_cell}')
+
     cellid[list12]=range(self.number_cell) #range(cellid[list12].shape[0])
     for i_value in tqdm(rho_descending_order):
         if cellid[int(i_value)]==-1: