Update Colab demo notebook

notebooks/Colab_inference_demo.ipynb

@@ -7,7 +7,7 @@
     "id": "view-in-github"
    },
    "source": [
-    "<a href=\"https://colab.research.google.com/github/MMathisLab/CellSeg3d/blob/main/Notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+    "<a href=\"https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3d/blob/main/notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
    ]
   },
   {
@@ -53,9 +53,94 @@
    },
    "outputs": [],
    "source": [
-    "# @markdown ##Install CellSeg3D and grab demo data\n",
-    "!git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git --branch main --single-branch ./CellSeg3D\n",
-    "!pip install napari-cellseg3d"
+    "# @markdown ## Install CellSeg3D only if needed\n",
+    "\n",
+    "import os\n",
+    "import shutil\n",
+    "import subprocess\n",
+    "import sys\n",
+    "from pathlib import Path\n",
+    "\n",
+    "\n",
+    "def run(cmd, **kwargs):\n",
+    "    print(\"+\", \" \".join(cmd))\n",
+    "    subprocess.check_call(cmd, **kwargs)\n",
+    "\n",
+    "\n",
+    "def cellseg3d_ok():\n",
+    "    try:\n",
+    "        import napari_cellseg3d\n",
+    "        from napari_cellseg3d.dev_scripts import remote_inference\n",
+    "\n",
+    "        print(\"CellSeg3D import OK.\")\n",
+    "        return True\n",
+    "\n",
+    "    except Exception as e:\n",
+    "        print(\"CellSeg3D import failed:\")\n",
+    "        print(type(e).__name__, e)\n",
+    "        return False\n",
+    "\n",
+    "\n",
+    "if not cellseg3d_ok():\n",
+    "    print(\"Installing CellSeg3D...\")\n",
+    "\n",
+    "    if shutil.which(\"uv\") is None:\n",
+    "        run([sys.executable, \"-m\", \"pip\", \"install\", \"-q\", \"uv\"])\n",
+    "    else:\n",
+    "        print(\"uv already installed.\")\n",
+    "\n",
+    "    if not Path(\"CellSeg3D\").is_dir():\n",
+    "        run(\n",
+    "            [\n",
+    "                \"git\",\n",
+    "                \"clone\",\n",
+    "                \"https://github.com/AdaptiveMotorControlLab/CellSeg3D.git\",\n",
+    "                \"--branch\",\n",
+    "                \"main\",\n",
+    "                \"--single-branch\",\n",
+    "                \"./CellSeg3D\",\n",
+    "            ]\n",
+    "        )\n",
+    "    else:\n",
+    "        print(\"CellSeg3D repo already cloned.\")\n",
+    "\n",
+    "    run(\n",
+    "        [\n",
+    "            \"uv\",\n",
+    "            \"pip\",\n",
+    "            \"install\",\n",
+    "            \"--system\",\n",
+    "            \"napari-cellseg3d\",\n",
+    "        ]\n",
+    "    )\n",
+    "\n",
+    "    print(\"Restarting runtime to reload installed binary dependencies...\")\n",
+    "    print(\n",
+    "        \"This will be shown as a crash, but this is expected. Please simply run the notebook again from the beginning after the runtime restarts.\"\n",
+    "    )\n",
+    "\n",
+    "    os.kill(os.getpid(), 9)\n",
+    "\n",
+    "else:\n",
+    "    print(\"CellSeg3D already available — skipping install and restart.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n",
+    "<div style=\"\n",
+    "  padding: 12px 16px;\n",
+    "  border-left: 5px solid #f59e0b;\n",
+    "  border-radius: 6px;\n",
+    "  margin: 12px 0;\n",
+    "\">\n",
+    "  <b>⚠️ Runtime restart is required after installation</b><br>\n",
+    "The runtime must be restarted after installing CellSeg3D to use the newly installed package. \n",
+    "\n",
+    "<b>The notebook will \"crash\" after installing, but this is expected, you may simply run the notebook again from the beginning after the runtime restarts.</b>\n",
+    "</div>"
    ]
   },
   {