Merge pull request #18 from berenslab/syns

Contact sites detection

Author: huangziwei

.github/media/contacts-meshes-with-patches.png

@@ -33,25 +33,25 @@
      "output_type": "stream",
      "text": [
       "[skeliner] starting skeletonisation (636,684 vertices, 1,274,227 faces)\n",
-      " ↳  build surface graph                          … 2.96 s\n",
-      " ↳  bin surface vertices by geodesic distance    … 2.57 s\n",
-      " ↳  compute bin centroids and radii              … 3.70 s\n",
+      " ↳  build surface graph                          … 3.06 s\n",
+      " ↳  bin surface vertices by geodesic distance    … 2.35 s\n",
+      " ↳  compute bin centroids and radii              … 4.71 s\n",
       " ↳  post-skeletonization soma detection          … 0.17 s\n",
       "      └─ Found soma at [951101.3, 1089465.3, 33282.6]\n",
       "      └─ (r =  7604.1, 4358.5, 2905.8)\n",
-      " ↳  map mesh faces to skeleton edges             … 0.43 s\n",
-      " ↳  merge redundant near-soma nodes              … 0.45 s\n",
+      " ↳  map mesh faces to skeleton edges             … 0.41 s\n",
+      " ↳  merge redundant near-soma nodes              … 0.62 s\n",
       "      └─ 68 nodes merged into soma\n",
       "      └─ Moved soma to [951156.9, 1087872.5, 33687.0]\n",
       "      └─ (r =  9015.2, 6155.3, 2758.3)\n",
       " ↳  bridge skeleton gaps                         … 0.15 s\n",
-      " ↳  build global minimum-spanning tree           … 0.07 s\n",
-      " ↳  prune tiny neurites                          … 0.53 s\n",
+      " ↳  build global minimum-spanning tree           … 0.06 s\n",
+      " ↳  prune tiny neurites                          … 0.55 s\n",
       "      └─ Merged 55 peri-soma nodes into soma \n",
       "      └─ Moved soma to [951582.4, 1086616.5, 34106.3]\n",
       "      └─ (r =  8441.2, 5798.7, 2761.2)\n",
       "      └─ Merged 416 single-node branches (416 edges).\n",
-      "TOTAL (soma + core + post)                       … 11.02 s (0.17 + 9.50 + 1.35)\n",
+      "TOTAL (soma + core + post)                       … 12.07 s (0.17 + 10.38 + 1.52)\n",
       "(8,921 nodes, 8,920 edges)\n"
      ]
     }
@@ -63,8 +63,10 @@
     "    collapse_soma=True, \n",
     "    bridge_gaps=True, \n",
     "    prune_tiny_neurites=True, \n",
+    "    # --- meta data ---\n",
     "    unit=\"nm\", # mesh unit\n",
     "    id=seg_id,\n",
+    "    # --- Optional ---\n",
     "    verbose=True,\n",
     ")"
    ]
@@ -140,13 +142,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Last updated: 2025-07-04 08:44:00CEST\n",
+      "Last updated: 2025-09-02 15:56:00CEST\n",
       "\n",
       "Python implementation: CPython\n",
       "Python version       : 3.11.11\n",
       "IPython version      : 9.2.0\n",
       "\n",
-      "skeliner: 0.1.9\n",
+      "skeliner: 0.1.11\n",
       "\n",
       "Watermark: 2.5.0\n",
       "\n"
@@ -161,7 +163,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "skeliner",
+   "display_name": "skeliner (3.11.11)",
    "language": "python",
    "name": "python3"
   },