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bendichter merged 1 commit into from
Jun 16, 2026
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001550 PaganLab: Colab-ready behavior + optogenetics notebooks #175

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344 changes: 172 additions & 172 deletions 001550/PaganLab/01_behavior_demo.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@
"id": "38b72d00",
"metadata": {},
"source": [
"## Installing requirements",
"",
"## Installing requirements\n",
"\n",
"The cell below installs every Python package needed to run this notebook, at fully pinned versions, using [`uv`](https://github.com/astral-sh/uv) for fast resolution. In Colab the cell is collapsed by default — click the ▶ button to run it."
]
},
Expand All @@ -40,174 +40,174 @@
"execution_count": null,
"outputs": [],
"source": [
"#@title Installing requirements (click ▶ to run) { display-mode: \"form\" }",
"# Colab provides Python 3.12. We install with `uv --system` because Colab's",
"# kernel runs outside a virtualenv. All versions (direct + transitive) are",
"# pinned below so the notebook is reproducible regardless of resolver drift.",
"!pip install -q uv",
"!uv pip install --system \\",
" \"acres==0.5.0\" \\",
" \"aiohappyeyeballs==2.6.1\" \\",
" \"aiohttp==3.13.5\" \\",
" \"aiosignal==1.4.0\" \\",
" \"annotated-types==0.7.0\" \\",
" \"anyio==4.13.0\" \\",
" \"argon2-cffi==25.1.0\" \\",
" \"argon2-cffi-bindings==25.1.0\" \\",
" \"arrow==1.4.0\" \\",
" \"asciitree==0.3.3\" \\",
" \"attrs==26.1.0\" \\",
" \"backcall==0.2.0\" \\",
" \"beautifulsoup4==4.13.5\" \\",
" \"bids-validator-deno==2.4.1\" \\",
" \"bidsschematools==1.2.2\" \\",
" \"bleach==6.3.0\" \\",
" \"blessed==1.38.0\" \\",
" \"certifi==2026.4.22\" \\",
" \"cffi==2.0.0\" \\",
" \"charset-normalizer==3.4.7\" \\",
" \"ci-info==0.4.0\" \\",
" \"click==8.1.8\" \\",
" \"click-didyoumean==0.3.1\" \\",
" \"contourpy==1.3.3\" \\",
" \"cryptography==43.0.3\" \\",
" \"cycler==0.12.1\" \\",
" \"dandi==0.76.4\" \\",
" \"dandischema==0.12.1\" \\",
" \"debugpy==1.8.15\" \\",
" \"decorator==4.4.2\" \\",
" \"defusedxml==0.7.1\" \\",
" \"deprecated==1.3.1\" \\",
" \"dnspython==2.8.0\" \\",
" \"email-validator==2.3.0\" \\",
" \"entrypoints==0.4\" \\",
" \"etelemetry==0.3.1\" \\",
" \"fasteners==0.20\" \\",
" \"fastjsonschema==2.21.2\" \\",
" \"fonttools==4.62.1\" \\",
" \"fqdn==1.5.1\" \\",
" \"frozenlist==1.8.0\" \\",
" \"fscacher==0.4.4\" \\",
" \"fsspec==2025.3.0\" \\",
" \"h5py==3.16.0\" \\",
" \"hdmf==4.3.1\" \\",
" \"humanize==4.15.0\" \\",
" \"idna==3.13\" \\",
" \"interleave==0.3.0\" \\",
" \"ipykernel==6.17.1\" \\",
" \"ipython==7.34.0\" \\",
" \"ipython-genutils==0.2.0\" \\",
" \"ipywidgets==7.7.1\" \\",
" \"isodate==0.7.2\" \\",
" \"isoduration==20.11.0\" \\",
" \"jaraco-classes==3.4.0\" \\",
" \"jaraco-context==6.1.2\" \\",
" \"jaraco-functools==4.4.0\" \\",
" \"jedi==0.20.0\" \\",
" \"jeepney==0.9.0\" \\",
" \"jinja2==3.1.6\" \\",
" \"joblib==1.5.3\" \\",
" \"jsonpointer==3.1.1\" \\",
" \"jsonschema==4.26.0\" \\",
" \"jsonschema-specifications==2025.9.1\" \\",
" \"jupyter-client==7.4.9\" \\",
" \"jupyter-core==5.9.1\" \\",
" \"jupyter-events==0.12.1\" \\",
" \"jupyter-server==2.14.0\" \\",
" \"jupyter-server-terminals==0.5.4\" \\",
" \"jupyterlab-pygments==0.3.0\" \\",
" \"jupyterlab-widgets==3.0.16\" \\",
" \"keyring==25.7.0\" \\",
" \"keyrings-alt==5.0.2\" \\",
" \"kiwisolver==1.5.0\" \\",
" \"lark==1.3.1\" \\",
" \"markupsafe==3.0.3\" \\",
" \"matplotlib==3.10.0\" \\",
" \"matplotlib-inline==0.2.1\" \\",
" \"mistune==3.2.0\" \\",
" \"ml-dtypes==0.5.4\" \\",
" \"more-itertools==10.8.0\" \\",
" \"multidict==6.7.1\" \\",
" \"natsort==8.4.0\" \\",
" \"nbclassic==1.3.3\" \\",
" \"nbclient==0.10.4\" \\",
" \"nbconvert==7.17.1\" \\",
" \"nbformat==5.10.4\" \\",
" \"ndx-ophys-devices==0.3.1\" \\",
" \"ndx-optogenetics==0.3.0\" \\",
" \"ndx-structured-behavior @ git+https://github.com/rly/ndx-structured-behavior.git@b31692480fa8c7e005dea7d843528582c02ef7e2\" \\",
" \"nest-asyncio==1.6.0\" \\",
" \"networkx==3.6.1\" \\",
" \"notebook==6.5.7\" \\",
" \"notebook-shim==0.2.4\" \\",
" \"numcodecs==0.15.1\" \\",
" \"numpy==2.0.2\" \\",
" \"nwbinspector==0.7.2\" \\",
" \"overrides==7.7.0\" \\",
" \"packaging==26.1\" \\",
" \"pandas==2.2.2\" \\",
" \"pandocfilters==1.5.1\" \\",
" \"parso==0.8.6\" \\",
" \"pexpect==4.9.0\" \\",
" \"pickleshare==0.7.5\" \\",
" \"pillow==11.3.0\" \\",
" \"platformdirs==4.9.6\" \\",
" \"prometheus-client==0.25.0\" \\",
" \"prompt-toolkit==3.0.52\" \\",
" \"propcache==0.4.1\" \\",
" \"psutil==5.9.5\" \\",
" \"ptyprocess==0.7.0\" \\",
" \"pycparser==3.0\" \\",
" \"pycryptodomex==3.23.0\" \\",
" \"pydantic==2.12.3\" \\",
" \"pydantic-core==2.41.4\" \\",
" \"pydantic-settings==2.14.0\" \\",
" \"pygments==2.20.0\" \\",
" \"pynwb==3.1.3\" \\",
" \"pyout==0.8.1\" \\",
" \"pyparsing==3.3.2\" \\",
" \"python-dateutil==2.9.0.post0\" \\",
" \"python-dotenv==1.2.2\" \\",
" \"python-json-logger==4.1.0\" \\",
" \"pytz==2025.2\" \\",
" \"pyyaml==6.0.3\" \\",
" \"pyzmq==26.2.1\" \\",
" \"referencing==0.37.0\" \\",
" \"remfile==0.1.13\" \\",
" \"requests==2.32.4\" \\",
" \"rfc3339-validator==0.1.4\" \\",
" \"rfc3986-validator==0.1.1\" \\",
" \"rfc3987==1.3.8\" \\",
" \"rfc3987-syntax==1.1.0\" \\",
" \"rpds-py==0.30.0\" \\",
" \"ruamel-yaml==0.19.1\" \\",
" \"scipy==1.16.3\" \\",
" \"secretstorage==3.5.0\" \\",
" \"semantic-version==2.10.0\" \\",
" \"send2trash==2.1.0\" \\",
" \"setuptools==75.2.0\" \\",
" \"six==1.17.0\" \\",
" \"soupsieve==2.8.3\" \\",
" \"tenacity==9.1.4\" \\",
" \"tensorstore==0.1.82\" \\",
" \"terminado==0.18.1\" \\",
" \"tinycss2==1.4.0\" \\",
" \"tornado==6.5.1\" \\",
" \"tqdm==4.67.3\" \\",
" \"traitlets==5.7.1\" \\",
" \"typing-extensions==4.15.0\" \\",
" \"typing-inspection==0.4.2\" \\",
" \"tzdata==2026.1\" \\",
" \"uri-template==1.3.0\" \\",
" \"urllib3==2.5.0\" \\",
" \"wcwidth==0.6.0\" \\",
" \"webcolors==25.10.0\" \\",
" \"webencodings==0.5.1\" \\",
" \"websocket-client==1.9.0\" \\",
" \"widgetsnbextension==3.6.10\" \\",
" \"wrapt==2.1.2\" \\",
" \"yarl==1.23.0\" \\",
" \"zarr==2.18.7\" \\",
"#@title Installing requirements (click ▶ to run) { display-mode: \"form\" }\n",
"# Colab provides Python 3.12. We install with `uv --system` because Colab's\n",
"# kernel runs outside a virtualenv. All versions (direct + transitive) are\n",
"# pinned below so the notebook is reproducible regardless of resolver drift.\n",
"!pip install -q uv\n",
"!uv pip install --system \\\n",
" \"acres==0.5.0\" \\\n",
" \"aiohappyeyeballs==2.6.1\" \\\n",
" \"aiohttp==3.13.5\" \\\n",
" \"aiosignal==1.4.0\" \\\n",
" \"annotated-types==0.7.0\" \\\n",
" \"anyio==4.13.0\" \\\n",
" \"argon2-cffi==25.1.0\" \\\n",
" \"argon2-cffi-bindings==25.1.0\" \\\n",
" \"arrow==1.4.0\" \\\n",
" \"asciitree==0.3.3\" \\\n",
" \"attrs==26.1.0\" \\\n",
" \"backcall==0.2.0\" \\\n",
" \"beautifulsoup4==4.13.5\" \\\n",
" \"bids-validator-deno==2.4.1\" \\\n",
" \"bidsschematools==1.2.2\" \\\n",
" \"bleach==6.3.0\" \\\n",
" \"blessed==1.38.0\" \\\n",
" \"certifi==2026.4.22\" \\\n",
" \"cffi==2.0.0\" \\\n",
" \"charset-normalizer==3.4.7\" \\\n",
" \"ci-info==0.4.0\" \\\n",
" \"click==8.1.8\" \\\n",
" \"click-didyoumean==0.3.1\" \\\n",
" \"contourpy==1.3.3\" \\\n",
" \"cryptography==43.0.3\" \\\n",
" \"cycler==0.12.1\" \\\n",
" \"dandi==0.76.4\" \\\n",
" \"dandischema==0.12.1\" \\\n",
" \"debugpy==1.8.15\" \\\n",
" \"decorator==4.4.2\" \\\n",
" \"defusedxml==0.7.1\" \\\n",
" \"deprecated==1.3.1\" \\\n",
" \"dnspython==2.8.0\" \\\n",
" \"email-validator==2.3.0\" \\\n",
" \"entrypoints==0.4\" \\\n",
" \"etelemetry==0.3.1\" \\\n",
" \"fasteners==0.20\" \\\n",
" \"fastjsonschema==2.21.2\" \\\n",
" \"fonttools==4.62.1\" \\\n",
" \"fqdn==1.5.1\" \\\n",
" \"frozenlist==1.8.0\" \\\n",
" \"fscacher==0.4.4\" \\\n",
" \"fsspec==2025.3.0\" \\\n",
" \"h5py==3.16.0\" \\\n",
" \"hdmf==4.3.1\" \\\n",
" \"humanize==4.15.0\" \\\n",
" \"idna==3.13\" \\\n",
" \"interleave==0.3.0\" \\\n",
" \"ipykernel==6.17.1\" \\\n",
" \"ipython==7.34.0\" \\\n",
" \"ipython-genutils==0.2.0\" \\\n",
" \"ipywidgets==7.7.1\" \\\n",
" \"isodate==0.7.2\" \\\n",
" \"isoduration==20.11.0\" \\\n",
" \"jaraco-classes==3.4.0\" \\\n",
" \"jaraco-context==6.1.2\" \\\n",
" \"jaraco-functools==4.4.0\" \\\n",
" \"jedi==0.20.0\" \\\n",
" \"jeepney==0.9.0\" \\\n",
" \"jinja2==3.1.6\" \\\n",
" \"joblib==1.5.3\" \\\n",
" \"jsonpointer==3.1.1\" \\\n",
" \"jsonschema==4.26.0\" \\\n",
" \"jsonschema-specifications==2025.9.1\" \\\n",
" \"jupyter-client==7.4.9\" \\\n",
" \"jupyter-core==5.9.1\" \\\n",
" \"jupyter-events==0.12.1\" \\\n",
" \"jupyter-server==2.14.0\" \\\n",
" \"jupyter-server-terminals==0.5.4\" \\\n",
" \"jupyterlab-pygments==0.3.0\" \\\n",
" \"jupyterlab-widgets==3.0.16\" \\\n",
" \"keyring==25.7.0\" \\\n",
" \"keyrings-alt==5.0.2\" \\\n",
" \"kiwisolver==1.5.0\" \\\n",
" \"lark==1.3.1\" \\\n",
" \"markupsafe==3.0.3\" \\\n",
" \"matplotlib==3.10.0\" \\\n",
" \"matplotlib-inline==0.2.1\" \\\n",
" \"mistune==3.2.0\" \\\n",
" \"ml-dtypes==0.5.4\" \\\n",
" \"more-itertools==10.8.0\" \\\n",
" \"multidict==6.7.1\" \\\n",
" \"natsort==8.4.0\" \\\n",
" \"nbclassic==1.3.3\" \\\n",
" \"nbclient==0.10.4\" \\\n",
" \"nbconvert==7.17.1\" \\\n",
" \"nbformat==5.10.4\" \\\n",
" \"ndx-ophys-devices==0.3.1\" \\\n",
" \"ndx-optogenetics==0.3.0\" \\\n",
" \"ndx-structured-behavior @ git+https://github.com/rly/ndx-structured-behavior.git@b31692480fa8c7e005dea7d843528582c02ef7e2\" \\\n",
" \"nest-asyncio==1.6.0\" \\\n",
" \"networkx==3.6.1\" \\\n",
" \"notebook==6.5.7\" \\\n",
" \"notebook-shim==0.2.4\" \\\n",
" \"numcodecs==0.15.1\" \\\n",
" \"numpy==2.0.2\" \\\n",
" \"nwbinspector==0.7.2\" \\\n",
" \"overrides==7.7.0\" \\\n",
" \"packaging==26.1\" \\\n",
" \"pandas==2.2.2\" \\\n",
" \"pandocfilters==1.5.1\" \\\n",
" \"parso==0.8.6\" \\\n",
" \"pexpect==4.9.0\" \\\n",
" \"pickleshare==0.7.5\" \\\n",
" \"pillow==11.3.0\" \\\n",
" \"platformdirs==4.9.6\" \\\n",
" \"prometheus-client==0.25.0\" \\\n",
" \"prompt-toolkit==3.0.52\" \\\n",
" \"propcache==0.4.1\" \\\n",
" \"psutil==5.9.5\" \\\n",
" \"ptyprocess==0.7.0\" \\\n",
" \"pycparser==3.0\" \\\n",
" \"pycryptodomex==3.23.0\" \\\n",
" \"pydantic==2.12.3\" \\\n",
" \"pydantic-core==2.41.4\" \\\n",
" \"pydantic-settings==2.14.0\" \\\n",
" \"pygments==2.20.0\" \\\n",
" \"pynwb==3.1.3\" \\\n",
" \"pyout==0.8.1\" \\\n",
" \"pyparsing==3.3.2\" \\\n",
" \"python-dateutil==2.9.0.post0\" \\\n",
" \"python-dotenv==1.2.2\" \\\n",
" \"python-json-logger==4.1.0\" \\\n",
" \"pytz==2025.2\" \\\n",
" \"pyyaml==6.0.3\" \\\n",
" \"pyzmq==26.2.1\" \\\n",
" \"referencing==0.37.0\" \\\n",
" \"remfile==0.1.13\" \\\n",
" \"requests==2.32.4\" \\\n",
" \"rfc3339-validator==0.1.4\" \\\n",
" \"rfc3986-validator==0.1.1\" \\\n",
" \"rfc3987==1.3.8\" \\\n",
" \"rfc3987-syntax==1.1.0\" \\\n",
" \"rpds-py==0.30.0\" \\\n",
" \"ruamel-yaml==0.19.1\" \\\n",
" \"scipy==1.16.3\" \\\n",
" \"secretstorage==3.5.0\" \\\n",
" \"semantic-version==2.10.0\" \\\n",
" \"send2trash==2.1.0\" \\\n",
" \"setuptools==75.2.0\" \\\n",
" \"six==1.17.0\" \\\n",
" \"soupsieve==2.8.3\" \\\n",
" \"tenacity==9.1.4\" \\\n",
" \"tensorstore==0.1.82\" \\\n",
" \"terminado==0.18.1\" \\\n",
" \"tinycss2==1.4.0\" \\\n",
" \"tornado==6.5.1\" \\\n",
" \"tqdm==4.67.3\" \\\n",
" \"traitlets==5.7.1\" \\\n",
" \"typing-extensions==4.15.0\" \\\n",
" \"typing-inspection==0.4.2\" \\\n",
" \"tzdata==2026.1\" \\\n",
" \"uri-template==1.3.0\" \\\n",
" \"urllib3==2.5.0\" \\\n",
" \"wcwidth==0.6.0\" \\\n",
" \"webcolors==25.10.0\" \\\n",
" \"webencodings==0.5.1\" \\\n",
" \"websocket-client==1.9.0\" \\\n",
" \"widgetsnbextension==3.6.10\" \\\n",
" \"wrapt==2.1.2\" \\\n",
" \"yarl==1.23.0\" \\\n",
" \"zarr==2.18.7\" \\\n",
" \"zarr-checksum==0.4.7\""
]
},
Expand All @@ -216,8 +216,8 @@
"id": "b2fbd796",
"metadata": {},
"source": [
"> **⚠️ Restart runtime after install**",
">",
"> **⚠️ Restart runtime after install**\n",
">\n",
"> The install may upgrade packages already loaded in the kernel. Go to **Runtime → Restart session**, then **Run all cells below** (skip this install cell on re-run)."
]
},
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