Make 39 notebooks Colab-ready: bootstrap cells + inline deps

000039/AllenInstitute/Create_manifest.ipynb

@@ -11,6 +11,45 @@
     "### This notebook creates a manifest that shows all of the assets within this dandiset, organized by their transgenic lines and recording locations"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dandi/example-notebooks/blob/master/000039/AllenInstitute/Create_manifest.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installing requirements\n",
+    "\n",
+    "The cell below installs the Python packages needed to run this notebook. It uses [`uv`](https://github.com/astral-sh/uv) for fast installs."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Expects Python 3.12 (Google Colab's default runtime as of 2026).\n",
+    "# Installs are scoped to the active interpreter via `uv pip install --system`,\n",
+    "# which is required because Colab runs the kernel outside a virtualenv.\n",
+    "!pip install -q uv\n",
+    "!uv pip install --system \\\n",
+    "    \"dandi>=0.60\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> **\u26a0\ufe0f Restart runtime after install**\n",
+    ">\n",
+    "> The install may upgrade packages already loaded in the kernel. Go to **Runtime \u2192 Restart session**, then **Run all cells below** (skip this install cell on re-run)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "5b1f2c68-262f-4d21-84fa-954d8a2acfb1",
@@ -88,7 +127,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 100/100 [01:49<00:00,  1.10s/it]\n"
+      "100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 100/100 [01:49<00:00,  1.10s/it]\n"
      ]
     }
    ],

000055/BruntonLab/peterson21/Fig_coarse_labels.ipynb

@@ -7,6 +7,62 @@
     "# Plot example coarse behavioral labelling trace"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dandi/example-notebooks/blob/master/000055/BruntonLab/peterson21/Fig_coarse_labels.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installing requirements\n",
+    "\n",
+    "The cell below installs the Python packages needed to run this notebook and fetches helper files that are colocated with the notebook in the repo."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Expects Python 3.12 (Google Colab's default runtime as of 2026).\n",
+    "# Installs are scoped to the active interpreter via `uv pip install --system`,\n",
+    "# which is required because Colab runs the kernel outside a virtualenv.\n",
+    "!pip install -q uv\n",
+    "!uv pip install --system \\\n",
+    "    \"pynwb>=2.8,<3\" \\\n",
+    "    \"hdmf<4\" \\\n",
+    "    \"dandi>=0.60\" \\\n",
+    "    \"h5py>=3.10\" \\\n",
+    "    \"numpy>=1.24\" \\\n",
+    "    \"pandas>=2.0\" \\\n",
+    "    \"matplotlib>=3.7\" \\\n",
+    "    \"seaborn>=0.13\" \\\n",
+    "    \"scipy>=1.11\" \\\n",
+    "    \"tqdm>=4.66\" \\\n",
+    "    \"ipywidgets>=8\" \\\n",
+    "    \"natsort>=8\" \\\n",
+    "    \"ndx-events<0.3\" \\\n",
+    "    \"nilearn>=0.10\" \\\n",
+    "    \"nwbwidgets>=0.11\" \\\n",
+    "    \"zarr<3\" \\\n",
+    "    \"ipython_genutils\"\n",
+    "!curl -sL -o plot_utils.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000055/BruntonLab/peterson21/plot_utils.py"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> **\u26a0\ufe0f Restart runtime after install**\n",
+    ">\n",
+    "> The install may upgrade packages already loaded in the kernel. Go to **Runtime \u2192 Restart session**, then **Run all cells below** (skip this install cell on re-run)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

000055/BruntonLab/peterson21/dashboard.ipynb

@@ -7,15 +7,65 @@
     "This notebook demonstrates how to run the dashboard, streaming data directly from the DANDI Archive. It is recommended to run this notebook on the [DANDI Hub](hub.dandiarchive.org) using the \"NWBStream\" environment."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dandi/example-notebooks/blob/master/000055/BruntonLab/peterson21/dashboard.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installing requirements\n",
+    "\n",
+    "The cell below installs the Python packages needed to run this notebook, including `brunton-lab-to-nwb` from its GitHub repo (it is not on PyPI)."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install dandi\n",
-    "%pip install git+https://github.com/catalystneuro/brunton-lab-to-nwb.git\n",
-    "%pip install nilearn"
+    "# Expects Python 3.12 (Google Colab's default runtime as of 2026).\n",
+    "# Installs are scoped to the active interpreter via `uv pip install --system`,\n",
+    "# which is required because Colab runs the kernel outside a virtualenv.\n",
+    "# NOTE: this notebook uses `driver='ros3'` to stream NWB from S3 \u2014 Colab's\n",
+    "# prebuilt h5py includes ROS3, but pip-installed h5py on other platforms may not.\n",
+    "!pip install -q uv\n",
+    "!uv pip install --system \\\n",
+    "    \"pynwb>=2.8,<3\" \\\n",
+    "    \"hdmf<4\" \\\n",
+    "    \"dandi>=0.60\" \\\n",
+    "    \"h5py>=3.10\" \\\n",
+    "    \"numpy>=1.24\" \\\n",
+    "    \"pandas>=2.0\" \\\n",
+    "    \"matplotlib>=3.7\" \\\n",
+    "    \"seaborn>=0.13\" \\\n",
+    "    \"scipy>=1.11\" \\\n",
+    "    \"tqdm>=4.66\" \\\n",
+    "    \"ipywidgets>=8\" \\\n",
+    "    \"natsort>=8\" \\\n",
+    "    \"ndx-events<0.3\" \\\n",
+    "    \"nilearn>=0.10\" \\\n",
+    "    \"nwbwidgets>=0.11\" \\\n",
+    "    \"zarr<3\" \\\n",
+    "    \"ipython_genutils\" \\\n",
+    "    \"bqplot>=0.12\" \\\n",
+    "    \"plotly>=5\" \\\n",
+    "    \"joblib>=1\" \\\n",
+    "    \"git+https://github.com/catalystneuro/brunton-lab-to-nwb.git\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> **\u26a0\ufe0f Restart runtime after install**\n",
+    ">\n",
+    "> The install may upgrade packages already loaded in the kernel. Go to **Runtime \u2192 Restart session**, then **Run all cells below** (skip this install cell on re-run)."
    ]
   },
   {

000108/chunglab/demo/2021-09-27_dandi-demo.ipynb

@@ -25,6 +25,53 @@
     "See the function, \"read\", below for how to simply read an arbitrary subvolume with stitching."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dandi/example-notebooks/blob/master/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installing requirements\n",
+    "\n",
+    "The cell below installs the Python packages needed to run this notebook. It uses [`uv`](https://github.com/astral-sh/uv) for fast installs."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Expects Python 3.12 (Google Colab's default runtime as of 2026).\n",
+    "# Installs are scoped to the active interpreter via `uv pip install --system`,\n",
+    "# which is required because Colab runs the kernel outside a virtualenv.\n",
+    "!pip install -q uv\n",
+    "!uv pip install --system \\\n",
+    "    \"dandi>=0.60\" \\\n",
+    "    \"h5py>=3.10\" \\\n",
+    "    \"hdf5plugin>=4\" \\\n",
+    "    \"numpy>=1.24\" \\\n",
+    "    \"matplotlib>=3.7\" \\\n",
+    "    \"Pillow>=10\" \\\n",
+    "    \"scikit-image>=0.22\" \\\n",
+    "    \"neuroglancer>=2.39\" \\\n",
+    "    \"requests>=2.31\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> **\u26a0\ufe0f Restart runtime after install**\n",
+    ">\n",
+    "> The install may upgrade packages already loaded in the kernel. Go to **Runtime \u2192 Restart session**, then **Run all cells below** (skip this install cell on re-run)."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

000108/chunglab/demo/dashboard.ipynb

@@ -327,6 +327,50 @@
     "output_notebook()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dandi/example-notebooks/blob/master/000108/chunglab/demo/dashboard.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installing requirements\n",
+    "\n",
+    "The cell below installs the Python packages needed to run this notebook. It uses [`uv`](https://github.com/astral-sh/uv) for fast installs."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Expects Python 3.12 (Google Colab's default runtime as of 2026).\n",
+    "# Installs are scoped to the active interpreter via `uv pip install --system`,\n",
+    "# which is required because Colab runs the kernel outside a virtualenv.\n",
+    "!pip install -q uv\n",
+    "!uv pip install --system \\\n",
+    "    \"dandi>=0.60\" \\\n",
+    "    \"numpy>=1.24\" \\\n",
+    "    \"pandas>=2.0\" \\\n",
+    "    \"matplotlib>=3.7\" \\\n",
+    "    \"seaborn>=0.13\" \\\n",
+    "    \"bokeh>=3.4\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> **\u26a0\ufe0f Restart runtime after install**\n",
+    ">\n",
+    "> The install may upgrade packages already loaded in the kernel. Go to **Runtime \u2192 Restart session**, then **Run all cells below** (skip this install cell on re-run)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "6f33476a-fa4e-408e-950a-3ed9a542b0c7",