Merge pull request #30 from angelolab/small_fix

Fixed a small bug in the cell analyzer
angelolab · Nov 22, 2024 · 089f9a2 · 089f9a2
2 parents 115a17d + 049e6af
commit 089f9a2
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Showing 2 changed files with 16 additions and 17 deletions.
diff --git a/src/nimbus_inference/cell_analyzer.py b/src/nimbus_inference/cell_analyzer.py
@@ -140,7 +140,7 @@ def create_composite_image(self, path_dict, add_boundaries=True):
         if self.segmentation_naming_convention and add_boundaries:
             fov_path = os.path.split(list(path_dict.values())[0])[0]
             seg_path = self.segmentation_naming_convention(fov_path)
-            seg_img = io.imread(seg_path)
+            seg_img = np.squeeze(io.imread(seg_path))
             seg_boundaries = find_boundaries(seg_img, mode='inner')
             individual_cell_boundary = seg_boundaries.copy()
             cell_mask = seg_img == self.cell_df[
@@ -166,7 +166,7 @@ def create_instance_image(self, path_dict, cell_id):
         # add overlay of instances
         fov_path = os.path.split(list(path_dict.values())[0])[0]
         seg_path = self.segmentation_naming_convention(fov_path)
-        seg_img = io.imread(seg_path)
+        seg_img = np.squeeze(io.imread(seg_path))
         seg_boundaries = find_boundaries(seg_img, mode='inner')
         seg_img[seg_boundaries] = 0
         seg_img_clipped = np.clip(seg_img, 0, 1) * 0.2

diff --git a/templates/3_analyze_individual_cells.ipynb b/templates/3_analyze_individual_cells.ipynb
@@ -54,21 +54,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "off_diagonal_df = pd.DataFrame(\n",
-    "    {\n",
-    "     \"Cell ID\": [1, 2, 3, 4],\n",
-    "     \"pixie_ct\": [\"Eosinophil\", \"Neutrophil\", \"Lymphocyte\", \"Monocyte\"],\n",
-    "     \"nimbus_ct\": [\"Neutrophil\", \"Lymphocyte\", \"Monocyte\", \"Eosinophil\"],\n",
-    "     \"fov\": [\"TMA32_R4C6\", \"TMA32_R4C6\", \"TMA32_R5C4\", \"TMA32_R5C4\"],\n",
-    "     \"label\": [451, 123, 234, 345],\n",
-    "     } \n",
-    ")\n",
-    "base_dir = os.path.normpath(\"C:/Users/lorenz/Desktop/angelo_lab/data/SPAIN_TNBC_fov_subset\")\n",
-    "tiff_dir = os.path.join(base_dir, \"image_data\")\n",
-    "deepcell_output_dir = os.path.join(base_dir, \"segmentation\", \"deepcell_output\")\n",
+    "off_diagonal_df = pd.read_csv(\"E:/angelo_lab/data/DCIS/cell_tables/potchara_data.csv\")\n",
+    "base_dir = os.path.normpath(\"E:/angelo_lab/data/DCIS\")\n",
+    "tiff_dir = os.path.join(base_dir, \"20230317_DCIS\", \"image_data\")\n",
+    "deepcell_output_dir = os.path.join(base_dir, \"deepcell_output\")\n",
     "segmentation_naming_convention = prep_naming_convention(deepcell_output_dir)\n",
     "\n",
-    "off_diagonal_df"
+    "fov_paths = [os.path.join(tiff_dir, f) for f in os.listdir(tiff_dir) if os.path.isdir(os.path.join(tiff_dir, f))]\n",
+    "# test segmentation_naming_convention\n",
+    "if os.path.exists(segmentation_naming_convention(fov_paths[0])):\n",
+    "    print(\"Segmentation data exists for fov 0 and naming convention is correct\")\n",
+    "else:\n",
+    "    print(\"Segmentation data does not exist for fov 0 or naming convention is incorrect\")\n",
+    "\n",
+    "off_diagonal_df[\"Cell ID\"] = off_diagonal_df.index.values"
    ]
   },
   {
@@ -89,7 +88,7 @@
     "                      output_dir=base_dir,\n",
     "                      segmentation_naming_convention=segmentation_naming_convention,\n",
     "                      img_width='600px',\n",
-    "                      context=200)\n",
+    "                      context=120)\n",
     "viewer.display()"
    ]
   }
@@ -110,7 +109,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.0"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,