diff --git a/.github/colab-preinstalled.txt b/.github/colab-preinstalled.txt new file mode 100644 index 0000000..cf4765d --- /dev/null +++ b/.github/colab-preinstalled.txt @@ -0,0 +1,653 @@ +# Google Colab's preinstalled package versions (Python 3.12 runtime). +# Source: https://github.com/googlecolab/backend-info (pip-freeze.txt) +# Last refreshed: 2026-05-13 +# +# This file is used as a uv-pip-compile --constraint when resolving each +# notebook's install-cell lock. Matching Colab's versions means the notebook +# install becomes a no-op for packages that are already at Colab's version, +# which is much faster AND avoids the "you must RESTART RUNTIME" prompt that +# numpy and other C-extension packages trigger when changed mid-session. +# +# When a notebook's direct deps say something incompatible with the Colab +# version (eg `numpy<2` for a notebook that uses np.NaN), the resolver +# falls back to ignoring constraints for that notebook — the lock will end +# up with non-Colab versions and the user WILL need to restart. That's the +# right trade: the notebook needs the older version to function. + +absl-py==1.4.0 +accelerate==1.13.0 +access==1.1.10.post3 +affine==2.4.0 +aiofiles==24.1.0 +aiohappyeyeballs==2.6.1 +aiohttp==3.13.5 +aiosignal==1.4.0 +aiosqlite==0.22.1 +alabaster==1.0.0 +albucore==0.0.24 +albumentations==2.0.8 +ale-py==0.11.2 +alembic==1.18.4 +altair==5.5.0 +annotated-doc==0.0.4 +annotated-types==0.7.0 +antlr4-python3-runtime==4.9.3 +anyio==4.13.0 +anywidget==0.9.21 +apsw==3.53.0.0 +apswutils==0.1.2 +argon2-cffi==25.1.0 +argon2-cffi-bindings==25.1.0 +array_record==0.8.3 +arrow==1.4.0 +arviz==0.22.0 +astropy==7.2.0 +astropy-iers-data==0.2026.4.20.0.58.15 +astunparse==1.6.3 +atpublic==5.1 +attrs==26.1.0 +audioread==3.1.0 +Authlib==1.6.11 +autograd==1.8.0 +babel==2.18.0 +backcall==0.2.0 +beartype==0.22.9 +beautifulsoup4==4.13.5 +betterproto==2.0.0b6 +bigframes==2.39.0 +bigquery-magics==0.14.0 +bleach==6.3.0 +blinker==1.9.0 +blis==1.3.3 +blobfile==3.2.0 +blosc2==4.1.2 +bokeh==3.8.2 +Bottleneck==1.4.2 +bqplot==0.12.45 +branca==0.8.2 +brotli==1.2.0 +CacheControl==0.14.4 +cachetools==6.2.6 +catalogue==2.0.10 +certifi==2026.4.22 +cffi==2.0.0 +chardet==5.2.0 +charset-normalizer==3.4.7 +clarabel==0.11.1 +click==8.3.3 +click-plugins==1.1.1.2 +cligj==0.7.2 +cloudpathlib==0.23.0 +cloudpickle==3.1.2 +cmake==3.31.10 +cmdstanpy==1.3.0 +colorcet==3.1.0 +colorlover==0.3.0 +community==1.0.0b1 +confection==1.3.3 +cons==0.4.7 +contourpy==1.3.3 +cramjam==2.11.0 +cryptography==43.0.3 +cufflinks==0.17.3 +curl_cffi==0.15.0 +cvxopt==1.3.2 +cvxpy==1.6.7 +cycler==0.12.1 +cyipopt==1.5.0 +cymem==2.0.13 +Cython==3.0.12 +dask==2026.3.0 +dataproc-spark-connect==1.1.0 +datasets==4.0.0 +db-dtypes==1.5.1 +debugpy==1.8.15 +decorator==4.4.2 +defusedxml==0.7.1 +deprecation==2.1.0 +diffusers==0.37.1 +dill==0.3.8 +distro==1.9.0 +dlib==19.24.6 +dm-tree==0.1.10 +docstring_parser==0.18.0 +docutils==0.21.2 +dopamine_rl==4.1.2 +duckdb==1.3.2 +earthengine-api==1.7.22 +easydict==1.13 +editdistance==0.8.1 +eerepr==0.1.2 +einops==0.8.2 +entrypoints==0.4 +esda==2.9.0 +et_xmlfile==2.0.0 +etils==1.14.0 +etuples==0.3.10 +Farama-Notifications==0.0.4 +fastai==2.8.7 +fastapi==0.136.1 +fastcore==1.12.42 +fastdownload==0.0.7 +fastjsonschema==2.21.2 +fastlite==0.2.4 +fastprogress==1.1.5 +fasttransform==0.0.2 +ffmpy==1.0.0 +filelock==3.29.0 +fiona==1.10.1 +firebase-admin==6.9.0 +Flask==3.1.3 +flatbuffers==25.12.19 +flax==0.11.2 +folium==0.20.0 +fonttools==4.62.1 +fqdn==1.5.1 +frozendict==2.4.7 +frozenlist==1.8.0 +fsspec==2025.3.0 +future==1.0.0 +gast==0.7.0 +gcsfs==2025.3.0 +GDAL==3.8.4 +gdown==5.2.2 +geemap==0.37.2 +geocoder==1.38.1 +geographiclib==2.1 +geopandas==1.1.3 +geopy==2.4.1 +giddy==2.3.6 +gin-config==0.5.0 +gitdb==4.0.12 +GitPython==3.1.47 +glob2==0.7 +google==3.0.0 +google-adk==1.29.0 +google-ai-generativelanguage==0.6.15 +google-api-core==2.30.3 +google-api-python-client==2.194.0 +google-auth==2.47.0 +google-auth-httplib2==0.3.1 +google-auth-oauthlib==1.3.1 +google-cloud-aiplatform==1.148.1 +google-cloud-appengine-logging==1.9.0 +google-cloud-audit-log==0.5.0 +google-cloud-bigquery==3.41.0 +google-cloud-bigquery-connection==1.21.0 +google-cloud-bigquery-storage==2.37.0 +google-cloud-bigtable==2.36.0 +google-cloud-core==2.5.1 +google-cloud-dataplex==2.18.0 +google-cloud-dataproc==5.27.0 +google-cloud-datastore==2.24.0 +google-cloud-discoveryengine==0.13.12 +google-cloud-firestore==2.27.0 +google-cloud-functions==1.23.0 +google-cloud-iam==2.22.0 +google-cloud-language==2.20.0 +google-cloud-logging==3.15.0 +google-cloud-monitoring==2.30.0 +google-cloud-pubsub==2.37.0 +google-cloud-resource-manager==1.17.0 +google-cloud-secret-manager==2.27.0 +google-cloud-spanner==3.65.0 +google-cloud-speech==2.38.0 +google-cloud-storage==3.10.1 +google-cloud-trace==1.19.0 +google-cloud-translate==3.26.0 +google-crc32c==1.8.0 +google-genai==1.68.0 +google-generativeai==0.8.6 +google-pasta==0.2.0 +google-resumable-media==2.8.2 +googleapis-common-protos==1.74.0 +googledrivedownloader==1.1.0 +gradio==5.50.0 +gradio_client==1.14.0 +grain==0.2.16 +graphviz==0.21 +greenlet==3.4.0 +groovy==0.1.2 +grpc-google-iam-v1==0.14.4 +grpc-interceptor==0.15.4 +grpcio==1.80.0 +grpcio-status==1.71.2 +grpclib==0.4.9 +gspread==6.2.1 +gspread-dataframe==4.0.0 +gym==0.25.2 +gym-notices==0.1.0 +gymnasium==1.3.0 +h11==0.16.0 +h2==4.3.0 +h5netcdf==1.8.1 +h5py==3.16.0 +hdbscan==0.8.42 +hf-xet==1.4.3 +highspy==1.14.0 +holidays==0.95 +holoviews==1.22.1 +hpack==4.1.0 +html5lib==1.1 +httpcore==1.0.9 +httpimport==1.4.1 +httplib2==0.31.2 +httptools==0.7.1 +httpx==0.28.1 +httpx-sse==0.4.3 +huggingface_hub==1.11.0 +humanize==4.15.0 +hyperframe==6.1.0 +hyperopt==0.2.7 +ibis-framework==9.5.0 +idna==3.13 +ImageIO==2.37.3 +imageio-ffmpeg==0.6.0 +imagesize==2.0.0 +imbalanced-learn==0.14.1 +immutabledict==4.3.1 +importlib_metadata==8.7.1 +importlib_resources==7.1.0 +imutils==0.5.4 +inequality==1.1.2 +inflect==7.5.0 +iniconfig==2.3.0 +intel-cmplr-lib-ur==2025.3.3 +intel-openmp==2025.3.3 +ipyevents==2.0.4 +ipyfilechooser==0.6.0 +ipykernel==6.17.1 +ipyleaflet==0.20.0 +ipyparallel==8.8.0 +ipython==7.34.0 +ipython-genutils==0.2.0 +ipython-sql==0.5.0 +ipywidgets==7.7.1 +isoduration==20.11.0 +itsdangerous==2.2.0 +jaraco.classes==3.4.0 +jaraco.context==6.1.2 +jaraco.functools==4.4.0 +jax==0.7.2 +jaxlib==0.7.2 +jeepney==0.9.0 +jieba==0.42.1 +Jinja2==3.1.6 +jiter==0.14.0 +joblib==1.5.3 +jsonpatch==1.33 +jsonpickle==4.1.1 +jsonpointer==3.1.1 +jsonschema==4.26.0 +jsonschema-specifications==2025.9.1 +jupyter-console==6.6.3 +jupyter-events==0.12.1 +jupyter-leaflet==0.20.0 +jupyter_client==7.4.9 +jupyter_core==5.9.1 +jupyter_server==2.14.0 +jupyter_server_terminals==0.5.4 +jupyterlab_pygments==0.3.0 +jupyterlab_widgets==3.0.16 +jupytext==1.19.1 +kaggle==2.0.2 +kagglehub==1.0.0 +kagglesdk==0.1.20 +keras==3.13.2 +keras-hub==0.26.0 +keras-nlp==0.26.0 +keyring==25.7.0 +keyrings.google-artifactregistry-auth==1.1.2 +kiwisolver==1.5.0 +langchain==1.2.15 +langchain-core==1.3.1 +langgraph==1.1.9 +langgraph-checkpoint==4.0.2 +langgraph-prebuilt==1.0.10 +langgraph-sdk==0.3.13 +langsmith==0.7.34 +lark==1.3.1 +lazy-loader==0.5 +libclang==18.1.1 +libpysal==4.14.1 +librosa==0.11.0 +lightgbm==4.6.0 +linkify-it-py==2.1.0 +llvmlite==0.43.0 +locket==1.0.0 +logical-unification==0.4.7 +lxml==6.1.0 +Mako==1.3.11 +mapclassify==2.10.0 +Markdown==3.10.2 +markdown-it-py==4.0.0 +MarkupSafe==3.0.3 +matplotlib==3.10.0 +matplotlib-inline==0.2.1 +matplotlib-venn==1.1.2 +mcp==1.27.0 +mdit-py-plugins==0.5.0 +mdurl==0.1.2 +mgwr==2.2.1 +miniKanren==1.0.5 +missingno==0.5.2 +mistune==3.2.0 +mizani==0.13.5 +mkl==2025.3.1 +ml_dtypes==0.5.4 +mlxtend==0.23.4 +mmh3==5.2.1 +momepy==0.11.0 +more-itertools==10.8.0 +moviepy==1.0.3 +mpmath==1.3.0 +msgpack==1.1.2 +multidict==6.7.1 +multipledispatch==1.0.0 +multiprocess==0.70.16 +multitasking==0.0.13 +murmurhash==1.0.15 +music21==9.9.1 +namex==0.1.0 +narwhals==2.20.0 +natsort==8.4.0 +nbclassic==1.3.3 +nbclient==0.10.4 +nbconvert==7.17.1 +nbformat==5.10.4 +ndindex==1.10.1 +nest-asyncio==1.6.0 +networkx==3.6.1 +nibabel==5.4.2 +nltk==3.9.1 +notebook==6.5.7 +notebook_shim==0.2.4 +numba==0.60.0 +numexpr==2.14.1 +numpy==2.0.2 +nvidia-nccl-cu12==2.30.4 +oauth2client==4.1.3 +oauthlib==3.3.1 +omegaconf==2.3.0 +openai==2.32.0 +opencv-contrib-python==4.13.0.92 +opencv-python==4.13.0.92 +opencv-python-headless==4.13.0.92 +openpyxl==3.1.5 +opt_einsum==3.4.0 +optax==0.2.8 +optree==0.19.0 +orbax-checkpoint==0.11.36 +orjson==3.11.8 +ormsgpack==1.12.2 +osqp==1.1.1 +overrides==7.7.0 +packaging==26.1 +pandas==2.2.2 +pandas-datareader==0.10.0 +pandas-gbq==0.30.0 +pandas-stubs==2.2.2.240909 +pandocfilters==1.5.1 +panel==1.8.10 +param==2.3.3 +parso==0.8.6 +parsy==2.2 +partd==1.4.2 +patsy==1.0.2 +peewee==4.0.5 +peft==0.19.1 +pexpect==4.9.0 +pickleshare==0.7.5 +pillow==11.3.0 +platformdirs==4.9.6 +plotly==5.24.1 +plotnine==0.14.5 +pluggy==1.6.0 +plum-dispatch==2.8.0 +pointpats==2.5.5 +polars==1.35.2 +pooch==1.9.0 +portpicker==1.5.2 +preshed==3.0.13 +prettytable==3.17.0 +proglog==0.1.12 +progressbar2==4.5.0 +prometheus_client==0.25.0 +promise==2.3 +prompt_toolkit==3.0.52 +propcache==0.4.1 +prophet==1.3.0 +proto-plus==1.27.2 +protobuf==5.29.6 +psutil==5.9.5 +psycopg2==2.9.12 +psygnal==0.15.1 +ptyprocess==0.7.0 +PuLP==3.3.0 +py-cpuinfo==9.0.0 +py4j==0.10.9.9 +pyarrow==18.1.0 +pyasn1==0.6.3 +pyasn1_modules==0.4.2 +pycocotools==2.0.11 +pycparser==3.0 +pycryptodomex==3.23.0 +pydantic==2.12.3 +pydantic-settings==2.14.0 +pydantic_core==2.41.4 +pydata-google-auth==1.9.1 +pydot==4.0.1 +pydotplus==2.0.2 +PyDrive2==1.21.3 +pydub==0.25.1 +pyerfa==2.0.1.5 +pygame==2.6.1 +pygit2==1.19.2 +Pygments==2.20.0 +pyiceberg==0.11.1 +PyJWT==2.12.1 +pymc==5.28.4 +pynndescent==0.6.0 +pyogrio==0.12.1 +pyomo==6.10.0 +PyOpenGL==3.1.10 +pyOpenSSL==24.2.1 +pyparsing==3.3.2 +pyperclip==1.11.0 +pyproj==3.7.2 +pyroaring==1.0.4 +pysal==25.7 +pyshp==3.0.3 +PySocks==1.7.1 +pyspark==4.0.2 +pytensor==2.38.2 +pytest==8.4.2 +python-box==7.4.1 +python-dateutil==2.9.0.post0 +python-dotenv==1.2.2 +python-fasthtml==0.12.50 +python-json-logger==4.1.0 +python-louvain==0.16 +python-multipart==0.0.26 +python-slugify==8.0.4 +python-snappy==0.7.3 +python-utils==3.9.1 +pytz==2025.2 +pyviz_comms==3.0.6 +PyWavelets==1.9.0 +PyYAML==6.0.3 +pyzmq==26.2.1 +quantecon==0.11.2 +rasterio==1.5.0 +rasterstats==0.20.0 +ratelim==0.1.6 +referencing==0.37.0 +regex==2025.11.3 +requests==2.32.4 +requests-oauthlib==2.0.0 +requests-toolbelt==1.0.0 +requirements-parser==0.9.0 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rfc3987-syntax==1.1.0 +rich==13.9.4 +roman-numerals==4.1.0 +roman-numerals-py==4.1.0 +rpds-py==0.30.0 +rpy2==3.5.17 +rsa==4.9.1 +rtree==1.4.1 +ruff==0.15.11 +safehttpx==0.1.7 +safetensors==0.7.0 +scikit-image==0.25.2 +scikit-learn==1.6.1 +scipy==1.16.3 +scooby==0.11.2 +scs==3.2.11 +seaborn==0.13.2 +SecretStorage==3.5.0 +segregation==2.5.4 +semantic-version==2.10.0 +Send2Trash==2.1.0 +sentence-transformers==5.4.1 +sentencepiece==0.2.1 +sentry-sdk==2.58.0 +setuptools==75.2.0 +shap==0.51.0 +shapely==2.1.2 +shellingham==1.5.4 +simple-parsing==0.1.8 +simplejson==4.1.0 +simsimd==6.5.16 +six==1.17.0 +sklearn-compat==0.1.5 +sklearn-pandas==2.2.0 +slicer==0.0.8 +smart_open==7.6.0 +smmap==5.0.3 +sniffio==1.3.1 +snowballstemmer==3.0.1 +soundfile==0.13.1 +soupsieve==2.8.3 +soxr==1.0.0 +spacy==3.8.14 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +spaghetti==1.7.6 +spanner-graph-notebook==1.1.10 +spglm==1.1.0 +Sphinx==8.2.3 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==2.0.0 +sphinxcontrib-serializinghtml==2.0.0 +spint==1.0.7 +splot==1.1.7 +spopt==0.7.0 +spreg==1.9.0 +SQLAlchemy==2.0.49 +sqlalchemy-spanner==1.17.3 +sqlglot==25.20.2 +sqlparse==0.5.5 +srsly==2.5.3 +sse-starlette==3.3.4 +stanio==0.5.1 +starlette==0.52.1 +statsmodels==0.14.6 +strictyaml==1.7.3 +stringzilla==4.6.0 +stumpy==1.13.0 +sympy==1.14.0 +tables==3.10.2 +tabulate==0.9.0 +tbb==2022.3.1 +tcmlib==1.4.1 +tenacity==9.1.4 +tensorboard==2.20.0 +tensorboard-data-server==0.7.2 +tensorflow==2.20.0 +tensorflow-datasets==4.9.9 +tensorflow-hub==0.16.1 +tensorflow-metadata==1.17.3 +tensorflow-probability==0.25.0 +tensorflow-text==2.20.1 +tensorstore==0.1.82 +termcolor==3.3.0 +terminado==0.18.1 +text-unidecode==1.3 +textblob==0.19.0 +tf-slim==1.1.0 +tf_keras==2.20.0 +thinc==8.3.13 +threadpoolctl==3.6.0 +tifffile==2026.4.11 +tiktoken==0.12.0 +timm==1.0.26 +tinycss2==1.4.0 +tobler==0.14.0 +tokenizers==0.22.2 +toml==0.10.2 +tomlkit==0.13.3 +toolz==0.12.1 +torchao==0.10.0 +torchdata==0.11.0 +torchsummary==1.5.1 +torchtune==0.6.1 +tornado==6.5.1 +tqdm==4.67.3 +traitlets==5.7.1 +traittypes==0.2.3 +transformers==5.0.0 +treescope==0.1.10 +tsfresh==0.21.1 +tweepy==4.16.0 +typeguard==4.5.1 +typer==0.24.2 +typer-slim==0.24.0 +types-pytz==2026.1.1.20260408 +types-setuptools==82.0.0.20260508 +typing-inspection==0.4.2 +typing_extensions==4.15.0 +tzdata==2026.1 +tzlocal==5.3.1 +uc-micro-py==2.0.0 +umap-learn==0.5.12 +umf==1.0.3 +uri-template==1.3.0 +uritemplate==4.2.0 +urllib3==2.5.0 +uuid_utils==0.14.1 +uvicorn==0.46.0 +uvloop==0.22.1 +vega-datasets==0.9.0 +wandb==0.26.1 +wasabi==1.1.3 +watchdog==6.0.0 +watchfiles==1.1.1 +wcwidth==0.6.0 +weasel==1.0.0 +webcolors==25.10.0 +webencodings==0.5.1 +websocket-client==1.9.0 +websockets==15.0.1 +Werkzeug==3.1.8 +wheel==0.47.0 +widgetsnbextension==3.6.10 +wordcloud==1.9.6 +wrapt==2.1.2 +xarray==2025.12.0 +xarray-einstats==0.10.0 +xgboost==3.2.0 +xlrd==2.0.2 +xxhash==3.6.0 +xyzservices==2026.3.0 +yarl==1.23.0 +ydf==0.15.0 +ydf_tf==2.20.0 +yellowbrick==1.5 +yfinance==0.2.66 +zipp==3.23.1 +zstandard==0.25.0 diff --git a/000108/chunglab/demo/dashboard.ipynb b/000108/chunglab/demo/dashboard.ipynb index ae64222..c2cd4a8 100644 --- a/000108/chunglab/demo/dashboard.ipynb +++ b/000108/chunglab/demo/dashboard.ipynb @@ -43,8 +43,8 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", - " \"bokeh==3.9.0\" \\\n", + " \"blessed==1.38.0\" \\\n", + " \"bokeh==3.8.2\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -52,7 +52,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -65,12 +65,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -87,34 +87,34 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", - " \"narwhals==2.21.0\" \\\n", + " \"narwhals==2.20.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\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", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", @@ -124,16 +124,16 @@ " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"xyzservices==2026.3.0\" \\\n", diff --git a/000402/MICrONS/demo/000402_microns_demo.ipynb b/000402/MICrONS/demo/000402_microns_demo.ipynb index 104ec09..72645e8 100644 --- a/000402/MICrONS/demo/000402_microns_demo.ipynb +++ b/000402/MICrONS/demo/000402_microns_demo.ipynb @@ -40,13 +40,12 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", - " \"bqplot==0.13.1\" \\\n", - " \"bqscales==0.3.7\" \\\n", + " \"blessed==1.38.0\" \\\n", + " \"bqplot==0.12.45\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -55,28 +54,27 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fonttools==4.62.1\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"gast==0.7.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"imageio==2.37.3\" \\\n", " \"importlib-metadata==4.13.0\" \\\n", " \"interleave==0.3.0\" \\\n", @@ -84,9 +82,8 @@ " \"ipydatawidgets==4.3.2\" \\\n", " \"ipyfilechooser==0.6.0\" \\\n", " \"ipympl==0.10.0\" \\\n", - " \"ipython==9.13.0\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipython-genutils==0.2.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", " \"ipyvolume==0.6.3\" \\\n", " \"ipyvue==1.12.0\" \\\n", " \"ipyvuetify==1.11.3\" \\\n", @@ -108,10 +105,10 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"lazy-loader==0.5\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-grayscalevolume==0.0.2\" \\\n", @@ -119,27 +116,26 @@ " \"ndx-spectrum==0.2.2\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", " \"nwbwidgets==0.11.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"plotly==5.13.1\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"py2vega==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -147,33 +143,34 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"pythreejs==2.4.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-image==0.26.0\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scikit-image==0.25.2\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", - " \"tifffile==2026.5.2\" \\\n", + " \"tifffile==2026.4.11\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"traittypes==0.2.3\" \\\n", " \"trimesh==4.12.2\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", diff --git a/000409/IBL/bwm_usage_notebook.ipynb b/000409/IBL/bwm_usage_notebook.ipynb index 0a56d3e..cbfe116 100644 --- a/000409/IBL/bwm_usage_notebook.ipynb +++ b/000409/IBL/bwm_usage_notebook.ipynb @@ -39,20 +39,20 @@ " \"aiosignal==1.4.0\" \\\n", " \"annotated-types==0.7.0\" \\\n", " \"anyio==4.13.0\" \\\n", - " \"anywidget==0.11.0\" \\\n", + " \"anywidget==0.9.21\" \\\n", " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"boto3==1.43.6\" \\\n", " \"botocore==1.43.6\" \\\n", " \"brainglobe-atlasapi==2.3.1\" \\\n", @@ -64,42 +64,41 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"colorlog==6.10.1\" \\\n", - " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.16.0\" \\\n", - " \"hdmf==4.2.0\" \\\n", + " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"iblatlas==0.10.0\" \\\n", + " \"iblatlas==1.0.0\" \\\n", " \"iblutil==1.20.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", - " \"ipywidgets==8.1.8\" \\\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", @@ -115,12 +114,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -130,55 +129,56 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"lark==1.3.1\" \\\n", - " \"lindi==0.4.6\" \\\n", - " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", + " \"llvmlite==0.43.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"mdurl==0.1.2\" \\\n", " \"meshio==5.3.5\" \\\n", - " \"mistune==3.2.1\" \\\n", + " \"mistune==3.2.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\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", " \"neo==0.14.4\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", - " \"numba==0.65.1\" \\\n", + " \"numba==0.60.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", - " \"nwb-video-widgets==0.1.7\" \\\n", + " \"numpy==2.0.2\" \\\n", + " \"nwb-video-widgets==0.1.5\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"one-api==3.4.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", + " \"one-api==3.5.2\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"psychofit==1.0.0.post0\" \\\n", " \"psygnal==0.15.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", - " \"pyarrow==24.0.0\" \\\n", + " \"pyarrow==18.1.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", - " \"pynapple==0.11.1\" \\\n", + " \"pynapple==0.11.2\" \\\n", " \"pynrrd==1.1.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -186,52 +186,52 @@ " \"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==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"quantities==0.16.4\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"ruff==0.15.12\" \\\n", + " \"ruff==0.15.11\" \\\n", " \"s3transfer==0.17.0\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", - " \"tifffile==2026.5.2\" \\\n", + " \"tifffile==2026.4.11\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"treelib==1.8.0\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\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==4.0.15\" \\\n", + " \"widgetsnbextension==3.6.10\" \\\n", " \"wrapt==2.1.2\" \\\n", - " \"xarray==2026.4.0\" \\\n", + " \"xarray==2025.12.0\" \\\n", " \"yarl==1.23.0\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" diff --git a/000458/AllenInstitute/reanalysis.ipynb b/000458/AllenInstitute/reanalysis.ipynb index 57c1983..a38e0cf 100644 --- a/000458/AllenInstitute/reanalysis.ipynb +++ b/000458/AllenInstitute/reanalysis.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,50 +84,51 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -147,6 +148,7 @@ }, { "cell_type": "markdown", + "id": "a45d02e4", "metadata": {}, "source": [ "# Reanalyzing Dandiset #000458" @@ -154,6 +156,7 @@ }, { "cell_type": "markdown", + "id": "c336eba7", "metadata": {}, "source": [ "This notebook works through some basic reanalysis of Dandiset #000458 to demonstrate how easy and straightforward the process is!\n", @@ -164,6 +167,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "d745dd6f", "metadata": {}, "outputs": [], "source": [ @@ -208,6 +212,7 @@ }, { "cell_type": "markdown", + "id": "ec4de67b", "metadata": {}, "source": [ "First we'll stream in the NWB file directly from DANDI using the function defined above." @@ -216,6 +221,7 @@ { "cell_type": "code", "execution_count": 2, + "id": "310f9069", "metadata": {}, "outputs": [ { @@ -1074,6 +1080,7 @@ }, { "cell_type": "markdown", + "id": "5b0ecdbe", "metadata": {}, "source": [ "From the nwbfile html render, we can see that\n", @@ -1084,6 +1091,7 @@ }, { "cell_type": "markdown", + "id": "0940182c", "metadata": {}, "source": [ "We'll need to select stimulation times from the awake and anesthetized period separately in order to make a comparison. To avoid any edge effects, we will omit 100s before and after isoflurane induction." @@ -1092,6 +1100,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "1614533c", "metadata": {}, "outputs": [ { @@ -1177,6 +1186,7 @@ }, { "cell_type": "markdown", + "id": "b6495a73", "metadata": {}, "source": [ "Now we will select 3 representative trials from each time period." @@ -1185,6 +1195,7 @@ { "cell_type": "code", "execution_count": 6, + "id": "11b3ebcb", "metadata": {}, "outputs": [ { @@ -1460,6 +1471,7 @@ }, { "cell_type": "markdown", + "id": "c861803c", "metadata": {}, "source": [ "To match Figure 4B, we will look specifically at primary somatosensory neurons (SSp)." @@ -1468,6 +1480,7 @@ { "cell_type": "code", "execution_count": 7, + "id": "7ef6e738", "metadata": {}, "outputs": [ { @@ -1487,6 +1500,7 @@ }, { "cell_type": "markdown", + "id": "f0631616", "metadata": {}, "source": [ "Finally, we will plot the spike times of all of the SSp units for each representative stimulation time (awake and anesthetized)." @@ -1495,6 +1509,7 @@ { "cell_type": "code", "execution_count": 8, + "id": "5300bf9a", "metadata": {}, "outputs": [ { @@ -1553,6 +1568,7 @@ }, { "cell_type": "markdown", + "id": "460c310e", "metadata": {}, "source": [ "As in Figure 4B of the paper, the raster plots show that the awake responses are more distributed in time (less synchronous) than the anesthetized responses." diff --git a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb index 095d435..d6cf3d1 100644 --- a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb +++ b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb @@ -43,14 +43,14 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\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", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", " \"deprecated==1.3.1\" \\\n", @@ -61,12 +61,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -82,46 +82,47 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"lindi==0.4.6\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -142,6 +143,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "5525f1b7", "metadata": {}, "outputs": [ { @@ -257,6 +259,7 @@ { "cell_type": "code", "execution_count": null, + "id": "874745fd", "metadata": {}, "outputs": [], "source": [] diff --git a/000458/FlatironInstitute/001_summarize_contents.ipynb b/000458/FlatironInstitute/001_summarize_contents.ipynb index 342efb8..404d183 100644 --- a/000458/FlatironInstitute/001_summarize_contents.ipynb +++ b/000458/FlatironInstitute/001_summarize_contents.ipynb @@ -43,14 +43,14 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\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", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", " \"deprecated==1.3.1\" \\\n", @@ -61,12 +61,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -82,46 +82,47 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"lindi==0.4.6\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -143,6 +144,7 @@ }, { "cell_type": "markdown", + "id": "62ab766f", "metadata": {}, "source": [ "## 000458 - summarize contents\n", @@ -153,6 +155,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "eed5b994", "metadata": {}, "outputs": [], "source": [ @@ -164,6 +167,7 @@ { "cell_type": "code", "execution_count": 11, + "id": "8650f18d", "metadata": {}, "outputs": [ { diff --git a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb index e2e02a4..b235e72 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb @@ -43,16 +43,16 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\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", - " \"colorcet==3.2.1\" \\\n", + " \"colorcet==3.1.0\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -66,12 +66,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -86,53 +86,54 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"neuroconv==0.7.2\" \\\n", + " \"neuroconv==0.7.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==1.26.4\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"parse==1.22.0\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.10.6\" \\\n", - " \"pydantic-core==2.27.2\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb index b658ef6..4d50305 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb @@ -40,11 +40,11 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"cellpose==3.1.1.3\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", @@ -54,19 +54,18 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cuda-bindings==13.2.0\" \\\n", " \"cuda-pathfinder==1.5.4\" \\\n", " \"cuda-toolkit==13.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastremap==1.19.0\" \\\n", " \"filelock==3.29.0\" \\\n", @@ -75,17 +74,16 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"imagecodecs==2026.1.14\" \\\n", " \"imageio==2.37.3\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -104,89 +102,88 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"lazy-loader==0.5\" \\\n", - " \"llvmlite==0.47.0\" \\\n", + " \"llvmlite==0.43.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"mpmath==1.3.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", - " \"numba==0.65.1\" \\\n", + " \"numba==0.60.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==1.26.4\" \\\n", - " \"nvidia-cublas==13.1.0.3\" \\\n", + " \"nvidia-cublas==13.1.1.3\" \\\n", " \"nvidia-cuda-cupti==13.0.85\" \\\n", " \"nvidia-cuda-nvrtc==13.0.88\" \\\n", " \"nvidia-cuda-runtime==13.0.96\" \\\n", - " \"nvidia-cudnn-cu13==9.19.0.56\" \\\n", + " \"nvidia-cudnn-cu13==9.20.0.48\" \\\n", " \"nvidia-cufft==12.0.0.61\" \\\n", " \"nvidia-cufile==1.15.1.6\" \\\n", " \"nvidia-curand==10.4.0.35\" \\\n", " \"nvidia-cusolver==12.0.4.66\" \\\n", " \"nvidia-cusparse==12.6.3.3\" \\\n", - " \"nvidia-cusparselt-cu13==0.8.0\" \\\n", - " \"nvidia-nccl-cu13==2.28.9\" \\\n", + " \"nvidia-cusparselt-cu13==0.8.1\" \\\n", + " \"nvidia-nccl-cu13==2.29.7\" \\\n", " \"nvidia-nvjitlink==13.0.88\" \\\n", " \"nvidia-nvshmem-cu13==3.4.5\" \\\n", " \"nvidia-nvtx==13.0.85\" \\\n", " \"nwbinspector==0.6.3\" \\\n", " \"opencv-python-headless==4.11.0.86\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"roifile==2026.2.10\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", " \"scikit-image==0.26.0\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"seaborn==0.13.2\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", - " \"setuptools==81.0.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"sympy==1.14.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tifffile==2026.3.3\" \\\n", - " \"torch==2.11.0\" \\\n", + " \"torch==2.12.0\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", - " \"triton==3.6.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", + " \"triton==3.7.0\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", @@ -210,6 +207,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "00ce282b", "metadata": {}, "outputs": [ { @@ -258,6 +256,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "01c442a1", "metadata": {}, "outputs": [], "source": [ @@ -620,6 +619,7 @@ { "cell_type": "code", "execution_count": 5, + "id": "12697228", "metadata": {}, "outputs": [ { @@ -641,6 +641,7 @@ { "cell_type": "code", "execution_count": null, + "id": "4badba73", "metadata": {}, "outputs": [], "source": [] diff --git a/000727/clandinin/simple_data_access/reading_data.ipynb b/000727/clandinin/simple_data_access/reading_data.ipynb index 91b8104..01eaa76 100644 --- a/000727/clandinin/simple_data_access/reading_data.ipynb +++ b/000727/clandinin/simple_data_access/reading_data.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,51 +84,52 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -148,6 +149,7 @@ }, { "cell_type": "markdown", + "id": "d9bb8405", "metadata": {}, "source": [ "# How to use the data in this dandiset\n", @@ -158,6 +160,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "728c0389", "metadata": {}, "outputs": [ { @@ -194,6 +197,7 @@ }, { "cell_type": "markdown", + "id": "43be2866", "metadata": {}, "source": [ "Now we pick the first of the assets above and stream it" @@ -202,6 +206,7 @@ { "cell_type": "code", "execution_count": 2, + "id": "6f7c14ac", "metadata": {}, "outputs": [ { @@ -361,6 +366,7 @@ }, { "cell_type": "markdown", + "id": "d029a99f", "metadata": {}, "source": [ "## Looking at the anatomical data" @@ -369,6 +375,7 @@ { "cell_type": "code", "execution_count": 3, + "id": "c14ad58f", "metadata": {}, "outputs": [ { @@ -465,6 +472,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "77af3b81", "metadata": {}, "outputs": [ { @@ -484,6 +492,7 @@ }, { "cell_type": "markdown", + "id": "c4405cf0", "metadata": {}, "source": [ "We have 100 samples of voxels (first dimension).\n", @@ -494,6 +503,7 @@ { "cell_type": "code", "execution_count": 5, + "id": "2debc6a9", "metadata": {}, "outputs": [ { @@ -519,6 +529,7 @@ { "cell_type": "code", "execution_count": 6, + "id": "fa1be61c", "metadata": {}, "outputs": [ { @@ -563,6 +574,7 @@ }, { "cell_type": "markdown", + "id": "58c7d1d1", "metadata": {}, "source": [ "## Looking at the FicTrac SpatialSeries data" @@ -571,6 +583,7 @@ { "cell_type": "code", "execution_count": 7, + "id": "a5f6d0dd", "metadata": {}, "outputs": [ { @@ -644,6 +657,7 @@ { "cell_type": "code", "execution_count": 8, + "id": "2a2da19d", "metadata": {}, "outputs": [ { diff --git a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb index 70174ed..e477418 100644 --- a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb +++ b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,51 +84,52 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -148,6 +149,7 @@ }, { "cell_type": "markdown", + "id": "f03cbf4f", "metadata": {}, "source": [ "

Navigating dandiset 000728: Visual Coding - Optical Physiology

" @@ -156,6 +158,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "3b8a04a9", "metadata": {}, "outputs": [], "source": [ @@ -179,6 +182,7 @@ { "cell_type": "code", "execution_count": 2, + "id": "fa9b97fb", "metadata": {}, "outputs": [], "source": [ @@ -187,6 +191,7 @@ }, { "cell_type": "markdown", + "id": "af32c8cb", "metadata": {}, "source": [ "
\n", @@ -198,6 +203,7 @@ }, { "cell_type": "markdown", + "id": "8ec49503", "metadata": {}, "source": [ "Alongside this notebook are included two JSON files that contain high-level metadata of the experiments - the conditions under which each was acquired.\n", @@ -210,6 +216,7 @@ { "cell_type": "code", "execution_count": 3, + "id": "c82ab90c", "metadata": {}, "outputs": [], "source": [ @@ -224,6 +231,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "b3b61a5c", "metadata": {}, "outputs": [], "source": [ @@ -235,6 +243,7 @@ }, { "cell_type": "markdown", + "id": "37a9d286", "metadata": {}, "source": [ "Start by getting all the areas, which are referred to as \"targeted structures\"." @@ -243,6 +252,7 @@ { "cell_type": "code", "execution_count": 5, + "id": "54d27abb", "metadata": {}, "outputs": [ { @@ -263,6 +273,7 @@ }, { "cell_type": "markdown", + "id": "b605ffd4", "metadata": {}, "source": [ "Then use a similar approach to get all imaging depths, all cre lines, all reporter lines, all stimuli, and all session types" @@ -271,6 +282,7 @@ { "cell_type": "code", "execution_count": 6, + "id": "424aebe0", "metadata": {}, "outputs": [ { @@ -304,6 +316,7 @@ { "cell_type": "code", "execution_count": 7, + "id": "009e8b86", "metadata": {}, "outputs": [ { @@ -329,6 +342,7 @@ { "cell_type": "code", "execution_count": 8, + "id": "4e465756", "metadata": {}, "outputs": [ { @@ -349,6 +363,7 @@ }, { "cell_type": "markdown", + "id": "572c4bee", "metadata": {}, "source": [ "The following figure is a good reference for describing the main differences between each session type with respect to the visual stimuli used." @@ -356,6 +371,7 @@ }, { "cell_type": "markdown", + "id": "ace33e3b", "metadata": {}, "source": [ "!['Diagram of containers'](http://alleninstitute.github.io/AllenSDK/_static/container_session_layout.png)" @@ -363,6 +379,7 @@ }, { "cell_type": "markdown", + "id": "86babe03", "metadata": {}, "source": [ "## 1.1 Experiment containers & sessions\n", @@ -374,6 +391,7 @@ }, { "cell_type": "markdown", + "id": "c167b745", "metadata": {}, "source": [ "
\n", @@ -386,6 +404,7 @@ { "cell_type": "code", "execution_count": 9, + "id": "0932e879", "metadata": {}, "outputs": [ { @@ -691,6 +710,7 @@ { "cell_type": "code", "execution_count": 10, + "id": "f1f14003", "metadata": {}, "outputs": [ { @@ -711,6 +731,7 @@ }, { "cell_type": "markdown", + "id": "09d0e93e", "metadata": {}, "source": [ "Let's look at one experiment container, imaged from Cux2, in VISp, from imaging depth 175 um." @@ -719,6 +740,7 @@ { "cell_type": "code", "execution_count": 11, + "id": "fdcf90f8", "metadata": {}, "outputs": [ { @@ -740,6 +762,7 @@ { "cell_type": "code", "execution_count": 12, + "id": "17e5078f", "metadata": {}, "outputs": [ { @@ -861,6 +884,7 @@ }, { "cell_type": "markdown", + "id": "bd772b8c", "metadata": {}, "source": [ "Let's get the id for the imaging session in this experiment container that used session type B." @@ -869,6 +893,7 @@ { "cell_type": "code", "execution_count": 13, + "id": "bd870532", "metadata": {}, "outputs": [ { @@ -889,6 +914,7 @@ }, { "cell_type": "markdown", + "id": "35ecadd5", "metadata": {}, "source": [ "
\n", @@ -901,6 +927,7 @@ }, { "cell_type": "markdown", + "id": "1c021306", "metadata": {}, "source": [ "Start by defining some quick helper functions..." @@ -909,6 +936,7 @@ { "cell_type": "code", "execution_count": 14, + "id": "c2f128ca", "metadata": {}, "outputs": [], "source": [ @@ -930,6 +958,7 @@ { "cell_type": "code", "execution_count": 15, + "id": "07eed2f1", "metadata": {}, "outputs": [], "source": [ @@ -946,6 +975,7 @@ }, { "cell_type": "markdown", + "id": "2a171ee2", "metadata": {}, "source": [ "Now we start streaming data directly from the DANDI Archive! Instead of downloading each entire file (usually around 500 MB; and there are 1518 files!), streaming simply requests the minimal amount of data needed to perform an immediate operation.\n", @@ -956,6 +986,7 @@ { "cell_type": "code", "execution_count": null, + "id": "14e6e3f2", "metadata": {}, "outputs": [], "source": [ @@ -967,6 +998,7 @@ }, { "cell_type": "markdown", + "id": "f26c31e5", "metadata": {}, "source": [ "Now we can load the NWB file from the dandiset that corresponds to our session ID." @@ -975,6 +1007,7 @@ { "cell_type": "code", "execution_count": 17, + "id": "8934d7b1", "metadata": {}, "outputs": [], "source": [ @@ -983,6 +1016,7 @@ }, { "cell_type": "markdown", + "id": "b9120e81", "metadata": {}, "source": [ "Try exploring the file contents interactively by expanding the dropdowns!" @@ -991,6 +1025,7 @@ { "cell_type": "code", "execution_count": 18, + "id": "f3b5ae4f", "metadata": {}, "outputs": [ { @@ -1499,6 +1534,7 @@ }, { "cell_type": "markdown", + "id": "395045ab", "metadata": {}, "source": [ "
\n", @@ -1511,6 +1547,7 @@ }, { "cell_type": "markdown", + "id": "5a56a923", "metadata": {}, "source": [ "Begin by defining some plotting functions to simplify cells throughout the later sections..." @@ -1519,6 +1556,7 @@ { "cell_type": "code", "execution_count": 19, + "id": "202341f6", "metadata": {}, "outputs": [], "source": [ @@ -1558,6 +1596,7 @@ { "cell_type": "code", "execution_count": 20, + "id": "87b847fd", "metadata": {}, "outputs": [], "source": [ @@ -1617,6 +1656,7 @@ { "cell_type": "code", "execution_count": 21, + "id": "b6202eaa", "metadata": {}, "outputs": [], "source": [ @@ -1673,6 +1713,7 @@ }, { "cell_type": "markdown", + "id": "ee7a58b6", "metadata": {}, "source": [ "## 3.0 Raw Motion Corrected Movies\n", @@ -1686,6 +1727,7 @@ }, { "cell_type": "markdown", + "id": "45e40372", "metadata": {}, "source": [ "
\n", @@ -1696,6 +1738,7 @@ { "cell_type": "code", "execution_count": 22, + "id": "421344a0", "metadata": {}, "outputs": [ { @@ -1803,6 +1846,7 @@ { "cell_type": "code", "execution_count": 23, + "id": "a00313f8", "metadata": {}, "outputs": [ { @@ -1897,6 +1941,7 @@ { "cell_type": "code", "execution_count": 24, + "id": "e95dea9b", "metadata": {}, "outputs": [ { @@ -1916,6 +1961,7 @@ }, { "cell_type": "markdown", + "id": "f569b540", "metadata": {}, "source": [ "That looks pretty noisy! The following sections will examine what the data looks like after it's been thoroughly cleaned." @@ -1923,6 +1969,7 @@ }, { "cell_type": "markdown", + "id": "9d17d26d", "metadata": {}, "source": [ "## 3.1 Maximum projection\n", @@ -1932,6 +1979,7 @@ { "cell_type": "code", "execution_count": 25, + "id": "2e1d3d87", "metadata": {}, "outputs": [ { @@ -1959,6 +2007,7 @@ { "cell_type": "code", "execution_count": 26, + "id": "02d45994", "metadata": {}, "outputs": [ { @@ -1978,6 +2027,7 @@ }, { "cell_type": "markdown", + "id": "3d6b2b40", "metadata": {}, "source": [ "
\n", @@ -1988,6 +2038,7 @@ { "cell_type": "code", "execution_count": 27, + "id": "df6cae44", "metadata": {}, "outputs": [ { @@ -2007,6 +2058,7 @@ }, { "cell_type": "markdown", + "id": "6163da67", "metadata": {}, "source": [ "## 3.2 PlaneSegmentation\n", @@ -2017,6 +2069,7 @@ { "cell_type": "code", "execution_count": 28, + "id": "6c77d5f2", "metadata": {}, "outputs": [ { @@ -2141,6 +2194,7 @@ }, { "cell_type": "markdown", + "id": "0123d8f4", "metadata": {}, "source": [ "Notice that each cell in the dataset has two IDs: a local ID specific to this table and session, and a unique global ID.\n", @@ -2153,6 +2207,7 @@ { "cell_type": "code", "execution_count": 29, + "id": "ea06e13b", "metadata": {}, "outputs": [ { @@ -2177,6 +2232,7 @@ { "cell_type": "code", "execution_count": 30, + "id": "57d1eaa8", "metadata": {}, "outputs": [], "source": [ @@ -2188,6 +2244,7 @@ }, { "cell_type": "markdown", + "id": "30c3fc1e", "metadata": {}, "source": [ "
\n", @@ -2200,6 +2257,7 @@ { "cell_type": "code", "execution_count": 31, + "id": "a7bcb8e1", "metadata": {}, "outputs": [ { @@ -2224,6 +2282,7 @@ } }, "cell_type": "markdown", + "id": "43913842", "metadata": {}, "source": [ "## 3.3 Segmented and Processed Traces\n", @@ -2240,6 +2299,7 @@ { "cell_type": "code", "execution_count": 32, + "id": "85dd9df9", "metadata": {}, "outputs": [ { @@ -2374,6 +2434,7 @@ { "cell_type": "code", "execution_count": 33, + "id": "877e5818", "metadata": {}, "outputs": [ { @@ -2543,6 +2604,7 @@ }, { "cell_type": "markdown", + "id": "6c1ee35d", "metadata": {}, "source": [ "Let's examine the $\\Delta F / F$ activity of the first ROI." @@ -2551,6 +2613,7 @@ { "cell_type": "code", "execution_count": 34, + "id": "67bf8fb0", "metadata": {}, "outputs": [], "source": [ @@ -2560,6 +2623,7 @@ }, { "cell_type": "markdown", + "id": "88c99819", "metadata": {}, "source": [ "
\n", @@ -2570,6 +2634,7 @@ { "cell_type": "code", "execution_count": 35, + "id": "653afd77", "metadata": {}, "outputs": [ { @@ -2591,6 +2656,7 @@ }, { "cell_type": "markdown", + "id": "d7563d9e", "metadata": {}, "source": [ "We can examine a narrower time window by slicing the frames (the first axis of the `data`) - but we have to take care to apply the same frame selection to both the `data` and the `timestamps`." @@ -2598,6 +2664,7 @@ }, { "cell_type": "markdown", + "id": "2fe3ba1e", "metadata": {}, "source": [ "
\n", @@ -2608,6 +2675,7 @@ { "cell_type": "code", "execution_count": 36, + "id": "8b51d4ae", "metadata": {}, "outputs": [ { @@ -2628,6 +2696,7 @@ { "cell_type": "code", "execution_count": 37, + "id": "c234c48d", "metadata": {}, "outputs": [ { @@ -2649,6 +2718,7 @@ }, { "cell_type": "markdown", + "id": "3afc76ba", "metadata": {}, "source": [ "
\n", @@ -2659,6 +2729,7 @@ { "cell_type": "code", "execution_count": 38, + "id": "bac8aca8", "metadata": {}, "outputs": [ { @@ -2684,6 +2755,7 @@ }, { "cell_type": "markdown", + "id": "7c7ebe21", "metadata": {}, "source": [ "It looks like different cells are active at different times. What could that be about?" @@ -2691,6 +2763,7 @@ }, { "cell_type": "markdown", + "id": "449e886c", "metadata": {}, "source": [ "## 3.4 Stimulus epochs\n", @@ -2700,6 +2773,7 @@ }, { "cell_type": "markdown", + "id": "1871181d", "metadata": {}, "source": [ "
\n", @@ -2710,6 +2784,7 @@ { "cell_type": "code", "execution_count": 39, + "id": "5668d67d", "metadata": {}, "outputs": [ { @@ -2820,6 +2895,7 @@ { "cell_type": "code", "execution_count": 40, + "id": "8f48744a", "metadata": {}, "outputs": [ { @@ -2842,6 +2918,7 @@ { "cell_type": "code", "execution_count": 41, + "id": "e6767496", "metadata": {}, "outputs": [ { @@ -2870,6 +2947,7 @@ }, { "cell_type": "markdown", + "id": "593bb1e9", "metadata": {}, "source": [ "## 3.5 Running speed\n", @@ -2880,6 +2958,7 @@ { "cell_type": "code", "execution_count": 42, + "id": "022c420b", "metadata": {}, "outputs": [ { @@ -2951,6 +3030,7 @@ { "cell_type": "code", "execution_count": 43, + "id": "67d4b017", "metadata": {}, "outputs": [ { @@ -2970,6 +3050,7 @@ }, { "cell_type": "markdown", + "id": "7b899e31", "metadata": {}, "source": [ "
\n", @@ -2980,6 +3061,7 @@ { "cell_type": "code", "execution_count": 44, + "id": "ba654c44", "metadata": {}, "outputs": [ { @@ -3012,6 +3094,7 @@ }, { "cell_type": "markdown", + "id": "23e30c1d", "metadata": {}, "source": [ "### Interesting things" @@ -3019,6 +3102,7 @@ }, { "cell_type": "markdown", + "id": "1d24b0f3", "metadata": {}, "source": [ "There are some interesting neurons here!\n", @@ -3033,6 +3117,7 @@ { "cell_type": "code", "execution_count": 45, + "id": "e038abf6", "metadata": {}, "outputs": [ { @@ -3066,6 +3151,7 @@ { "cell_type": "code", "execution_count": 46, + "id": "decd2f35", "metadata": {}, "outputs": [ { @@ -3099,6 +3185,7 @@ { "cell_type": "code", "execution_count": 47, + "id": "54e3f103", "metadata": {}, "outputs": [ { @@ -3131,6 +3218,7 @@ }, { "cell_type": "markdown", + "id": "f1efd7ee", "metadata": {}, "source": [ "### 3.6 Extracted events from $\\Delta F / F$ \n", @@ -3145,6 +3233,7 @@ { "cell_type": "code", "execution_count": 48, + "id": "26d21136", "metadata": {}, "outputs": [ { @@ -3270,6 +3359,7 @@ }, { "cell_type": "markdown", + "id": "1a10e309", "metadata": {}, "source": [ "
\n", @@ -3280,6 +3370,7 @@ { "cell_type": "code", "execution_count": 49, + "id": "cf67aa74", "metadata": {}, "outputs": [ { @@ -3308,6 +3399,7 @@ }, { "cell_type": "markdown", + "id": "af607960", "metadata": {}, "source": [ "
\n", @@ -3318,6 +3410,7 @@ { "cell_type": "code", "execution_count": 50, + "id": "871dda3e", "metadata": {}, "outputs": [ { @@ -3347,6 +3440,7 @@ }, { "cell_type": "markdown", + "id": "f251e409", "metadata": {}, "source": [ "
\n", @@ -3357,6 +3451,7 @@ { "cell_type": "code", "execution_count": 51, + "id": "10b45f7d", "metadata": {}, "outputs": [ { @@ -3389,6 +3484,7 @@ }, { "cell_type": "markdown", + "id": "027cecc9", "metadata": {}, "source": [ "### 3.7 Stimulus Module\n", @@ -3398,6 +3494,7 @@ }, { "cell_type": "markdown", + "id": "b5d6fbd7", "metadata": {}, "source": [ "### 3.7a Natural Scenes\n", @@ -3410,6 +3507,7 @@ { "cell_type": "code", "execution_count": 52, + "id": "dd026b59", "metadata": {}, "outputs": [ { @@ -3481,6 +3579,7 @@ { "cell_type": "code", "execution_count": 53, + "id": "a2c5cb91", "metadata": {}, "outputs": [ { @@ -3502,6 +3601,7 @@ { "cell_type": "code", "execution_count": 54, + "id": "116327e4", "metadata": {}, "outputs": [ { @@ -3522,6 +3622,7 @@ }, { "cell_type": "markdown", + "id": "9ce89ca2", "metadata": {}, "source": [ "The actual images and movies presented during the session area also included in the NWB file as the stimulus template.\n", @@ -3532,6 +3633,7 @@ { "cell_type": "code", "execution_count": 55, + "id": "df7b5d8c", "metadata": {}, "outputs": [ { @@ -3713,6 +3815,7 @@ { "cell_type": "code", "execution_count": 56, + "id": "78ac1405", "metadata": { "scrolled": true }, @@ -3897,6 +4000,7 @@ { "cell_type": "code", "execution_count": 57, + "id": "6eba04cd", "metadata": {}, "outputs": [ { @@ -3916,6 +4020,7 @@ }, { "cell_type": "markdown", + "id": "5f2e6551", "metadata": {}, "source": [ "
\n", @@ -3926,6 +4031,7 @@ { "cell_type": "code", "execution_count": 58, + "id": "060792b2", "metadata": {}, "outputs": [ { @@ -3947,6 +4053,7 @@ }, { "cell_type": "markdown", + "id": "2f45c948", "metadata": {}, "source": [ "Use the stimulus table to plot the responses of cell index 1 to image 101" @@ -3954,6 +4061,7 @@ }, { "cell_type": "markdown", + "id": "8cf99a39", "metadata": {}, "source": [ "### 3.7b Natural Movies\n", @@ -3964,6 +4072,7 @@ { "cell_type": "code", "execution_count": 59, + "id": "447a07de", "metadata": {}, "outputs": [ { @@ -4053,6 +4162,7 @@ { "cell_type": "code", "execution_count": 60, + "id": "8fce1d60", "metadata": { "scrolled": true }, @@ -4131,6 +4241,7 @@ { "cell_type": "code", "execution_count": 61, + "id": "ec001b50", "metadata": {}, "outputs": [ { @@ -4150,6 +4261,7 @@ }, { "cell_type": "markdown", + "id": "261c987c", "metadata": {}, "source": [ "
\n", @@ -4160,6 +4272,7 @@ { "cell_type": "code", "execution_count": 62, + "id": "9756f840", "metadata": {}, "outputs": [ { @@ -4181,6 +4294,7 @@ }, { "cell_type": "markdown", + "id": "b72fe162", "metadata": {}, "source": [ "### 3.7c Static Gratings\n", @@ -4191,6 +4305,7 @@ { "cell_type": "code", "execution_count": 63, + "id": "5ed95df0", "metadata": {}, "outputs": [ { @@ -4289,6 +4404,7 @@ }, { "cell_type": "markdown", + "id": "b15a3f43", "metadata": {}, "source": [ "
\n", @@ -4301,6 +4417,7 @@ { "cell_type": "code", "execution_count": 64, + "id": "9a8d07cf", "metadata": {}, "outputs": [ { @@ -4326,6 +4443,7 @@ }, { "cell_type": "markdown", + "id": "9c2a2df9", "metadata": {}, "source": [ "### 3.7 Drifting Gratings\n", @@ -4338,6 +4456,7 @@ { "cell_type": "code", "execution_count": 65, + "id": "9a302c0b", "metadata": {}, "outputs": [], "source": [ @@ -4349,6 +4468,7 @@ { "cell_type": "code", "execution_count": 66, + "id": "de6d93c1", "metadata": {}, "outputs": [ { @@ -4482,6 +4602,7 @@ { "cell_type": "code", "execution_count": 67, + "id": "8d8f9a1a", "metadata": {}, "outputs": [ { @@ -4507,6 +4628,7 @@ }, { "cell_type": "markdown", + "id": "00eddfa7", "metadata": {}, "source": [ "
\n", @@ -4518,6 +4640,7 @@ }, { "cell_type": "markdown", + "id": "18ab83bc", "metadata": {}, "source": [ "
\n", @@ -4530,6 +4653,7 @@ { "cell_type": "code", "execution_count": 68, + "id": "1311f737", "metadata": {}, "outputs": [], "source": [ @@ -4539,6 +4663,7 @@ { "cell_type": "code", "execution_count": 69, + "id": "bae2a97f", "metadata": {}, "outputs": [ { @@ -4583,6 +4708,7 @@ { "cell_type": "code", "execution_count": 70, + "id": "93a7c476", "metadata": {}, "outputs": [ { @@ -4625,6 +4751,7 @@ }, { "cell_type": "markdown", + "id": "dc8b7817", "metadata": {}, "source": [ "
\n", @@ -4636,6 +4763,7 @@ }, { "cell_type": "markdown", + "id": "d9512993", "metadata": {}, "source": [ "
\n", @@ -4646,6 +4774,7 @@ { "cell_type": "code", "execution_count": 71, + "id": "54a04e15", "metadata": {}, "outputs": [], "source": [ @@ -4672,6 +4801,7 @@ { "cell_type": "code", "execution_count": 72, + "id": "68b4c6e1", "metadata": {}, "outputs": [ { @@ -4691,6 +4821,7 @@ }, { "cell_type": "markdown", + "id": "0b84821c", "metadata": {}, "source": [ "
\n", @@ -4703,6 +4834,7 @@ { "cell_type": "code", "execution_count": 73, + "id": "6b58f4c3", "metadata": {}, "outputs": [], "source": [ @@ -4716,6 +4848,7 @@ { "cell_type": "code", "execution_count": 74, + "id": "eabf6c98", "metadata": {}, "outputs": [ { @@ -4735,6 +4868,7 @@ }, { "cell_type": "markdown", + "id": "8b9462da", "metadata": {}, "source": [ "
\n", @@ -4745,6 +4879,7 @@ { "cell_type": "code", "execution_count": 75, + "id": "b39e8449", "metadata": {}, "outputs": [], "source": [ @@ -4767,6 +4902,7 @@ { "cell_type": "code", "execution_count": 76, + "id": "af1fd95f", "metadata": {}, "outputs": [ { @@ -4786,6 +4922,7 @@ }, { "cell_type": "markdown", + "id": "e28294a8", "metadata": {}, "source": [ "
\n", @@ -4796,6 +4933,7 @@ { "cell_type": "code", "execution_count": 77, + "id": "4ad69940", "metadata": {}, "outputs": [ { @@ -4821,6 +4959,7 @@ }, { "cell_type": "markdown", + "id": "a0af4f5c", "metadata": {}, "source": [ "
\n", @@ -4832,6 +4971,7 @@ }, { "cell_type": "markdown", + "id": "50305c01", "metadata": {}, "source": [ "The Allen Brain Observatory - Visual Coding (Ophys) is a rich dataset that allows you to explore single cell and population responses across 6 cortical areas, 4 cortical layers, 14 transgenic Cre lines to a range of different visual stimuli.\n", @@ -4842,6 +4982,7 @@ { "cell_type": "code", "execution_count": null, + "id": "75e5dd01", "metadata": {}, "outputs": [], "source": [] diff --git a/000947/TurnerLab/public_demo/000947_demo.ipynb b/000947/TurnerLab/public_demo/000947_demo.ipynb index 04c6883..e38cb00 100644 --- a/000947/TurnerLab/public_demo/000947_demo.ipynb +++ b/000947/TurnerLab/public_demo/000947_demo.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", - " \"hdmf==4.2.0\" \\\n", + " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,29 +84,29 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"llvmlite==0.43.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-turner-metadata==0.1.0\" \\\n", - " \"numba==0.65.1\" \\\n", + " \"numba==0.60.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.7.1\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -114,30 +114,31 @@ " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb index 8d45776..678b9ba 100644 --- a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,52 +84,53 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-events==0.2.2\" \\\n", " \"ndx-fiber-photometry==0.1.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", @@ -151,6 +152,7 @@ }, { "cell_type": "markdown", + "id": "2bc416df", "metadata": {}, "source": [ "# Fiber Photometry Example Session" @@ -159,6 +161,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "b7f9de4b", "metadata": {}, "outputs": [], "source": [ @@ -169,6 +172,7 @@ }, { "cell_type": "markdown", + "id": "43f3bd83", "metadata": {}, "source": [ "This notebook showcases one example session from the 000971 dataset containing operant behavior and concurrent fiber photometry recordings." @@ -177,6 +181,7 @@ { "cell_type": "code", "execution_count": 2, + "id": "3ef95a3e", "metadata": {}, "outputs": [ { @@ -469,6 +474,7 @@ }, { "cell_type": "markdown", + "id": "1968f8c3", "metadata": {}, "source": [ "Retrieve Photometry and Behavioral Data" @@ -477,6 +483,7 @@ { "cell_type": "code", "execution_count": 3, + "id": "3f037d0a", "metadata": {}, "outputs": [], "source": [ @@ -501,6 +508,7 @@ }, { "cell_type": "markdown", + "id": "a7f88da3", "metadata": {}, "source": [ "Plot" @@ -509,6 +517,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "31b3057c", "metadata": {}, "outputs": [ { @@ -572,6 +581,7 @@ }, { "cell_type": "markdown", + "id": "749ddfc7", "metadata": {}, "source": [ "Zoom in for more detail" @@ -580,6 +590,7 @@ { "cell_type": "code", "execution_count": 5, + "id": "17467732", "metadata": {}, "outputs": [ { @@ -644,6 +655,7 @@ { "cell_type": "code", "execution_count": null, + "id": "d3b7361c", "metadata": {}, "outputs": [], "source": [] diff --git a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb index 1987fc8..5fe5344 100644 --- a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb @@ -33,106 +33,106 @@ "# 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", - " \"arrow==1.4.0\" \\\\\n", - " \"asciitree==0.3.3\" \\\\\n", - " \"attrs==26.1.0\" \\\\\n", - " \"bids-validator-deno==2.4.1\" \\\\\n", - " \"bidsschematools==1.2.2\" \\\\\n", - " \"blessed==1.39.0\" \\\\\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==48.0.0\" \\\\\n", - " \"cycler==0.12.1\" \\\\\n", - " \"dandi==0.74.3\" \\\\\n", - " \"dandischema==0.12.1\" \\\\\n", - " \"deprecated==1.3.1\" \\\\\n", - " \"dnspython==2.8.0\" \\\\\n", - " \"email-validator==2.3.0\" \\\\\n", - " \"etelemetry==0.3.1\" \\\\\n", - " \"fasteners==0.20\" \\\\\n", - " \"fonttools==4.62.1\" \\\\\n", - " \"fqdn==1.5.1\" \\\\\n", - " \"frozenlist==1.8.0\" \\\\\n", - " \"fscacher==0.4.4\" \\\\\n", - " \"fsspec==2026.4.0\" \\\\\n", - " \"h5py==3.16.0\" \\\\\n", - " \"hdmf==3.14.6\" \\\\\n", - " \"hdmf-zarr==0.11.3\" \\\\\n", - " \"humanize==4.15.0\" \\\\\n", - " \"idna==3.14\" \\\\\n", - " \"interleave==0.3.0\" \\\\\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", - " \"jeepney==0.9.0\" \\\\\n", - " \"joblib==1.5.3\" \\\\\n", - " \"jsonpointer==3.1.1\" \\\\\n", - " \"jsonschema==4.26.0\" \\\\\n", - " \"jsonschema-specifications==2025.9.1\" \\\\\n", - " \"keyring==25.7.0\" \\\\\n", - " \"keyrings-alt==5.0.2\" \\\\\n", - " \"kiwisolver==1.5.0\" \\\\\n", - " \"matplotlib==3.10.9\" \\\\\n", - " \"ml-dtypes==0.5.4\" \\\\\n", - " \"more-itertools==11.0.2\" \\\\\n", - " \"multidict==6.7.1\" \\\\\n", - " \"natsort==8.4.0\" \\\\\n", - " \"ndx-events==0.4.0\" \\\\\n", - " \"numcodecs==0.15.1\" \\\\\n", - " \"numpy==2.4.4\" \\\\\n", - " \"nwbinspector==0.6.3\" \\\\\n", - " \"packaging==26.2\" \\\\\n", - " \"pandas==3.0.3\" \\\\\n", - " \"pillow==12.2.0\" \\\\\n", - " \"platformdirs==4.9.6\" \\\\\n", - " \"propcache==0.5.2\" \\\\\n", - " \"pycparser==3.0\" \\\\\n", - " \"pycryptodomex==3.23.0\" \\\\\n", - " \"pydantic==2.13.4\" \\\\\n", - " \"pydantic-core==2.46.4\" \\\\\n", - " \"pydantic-settings==2.14.1\" \\\\\n", - " \"pynwb==2.8.3\" \\\\\n", - " \"pyout==0.8.1\" \\\\\n", - " \"pyparsing==3.3.2\" \\\\\n", - " \"python-dateutil==2.9.0.post0\" \\\\\n", - " \"python-dotenv==1.2.2\" \\\\\n", - " \"pyyaml==6.0.3\" \\\\\n", - " \"referencing==0.37.0\" \\\\\n", - " \"requests==2.34.0\" \\\\\n", - " \"rfc3339-validator==0.1.4\" \\\\\n", - " \"rfc3987==1.3.8\" \\\\\n", - " \"rpds-py==0.30.0\" \\\\\n", - " \"ruamel-yaml==0.19.1\" \\\\\n", - " \"scipy==1.17.1\" \\\\\n", - " \"secretstorage==3.5.0\" \\\\\n", - " \"semantic-version==2.10.0\" \\\\\n", - " \"six==1.17.0\" \\\\\n", - " \"tenacity==9.1.4\" \\\\\n", - " \"tensorstore==0.1.83\" \\\\\n", - " \"threadpoolctl==3.6.0\" \\\\\n", - " \"tqdm==4.67.3\" \\\\\n", - " \"typing-extensions==4.15.0\" \\\\\n", - " \"typing-inspection==0.4.2\" \\\\\n", - " \"tzdata==2026.2\" \\\\\n", - " \"uri-template==1.3.0\" \\\\\n", - " \"urllib3==2.7.0\" \\\\\n", - " \"wcwidth==0.7.0\" \\\\\n", - " \"webcolors==25.10.0\" \\\\\n", - " \"wrapt==2.1.2\" \\\\\n", - " \"yarl==1.23.0\" \\\\\n", - " \"zarr==2.18.7\" \\\\\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", + " \"arrow==1.4.0\" \\\n", + " \"asciitree==0.3.3\" \\\n", + " \"attrs==26.1.0\" \\\n", + " \"bids-validator-deno==2.4.1\" \\\n", + " \"bidsschematools==1.2.2\" \\\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==0.74.3\" \\\n", + " \"dandischema==0.12.1\" \\\n", + " \"deprecated==1.3.1\" \\\n", + " \"dnspython==2.8.0\" \\\n", + " \"email-validator==2.3.0\" \\\n", + " \"etelemetry==0.3.1\" \\\n", + " \"fasteners==0.20\" \\\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==5.0.1\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", + " \"humanize==4.15.0\" \\\n", + " \"idna==3.13\" \\\n", + " \"interleave==0.3.0\" \\\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", + " \"jeepney==0.9.0\" \\\n", + " \"joblib==1.5.3\" \\\n", + " \"jsonpointer==3.1.1\" \\\n", + " \"jsonschema==4.26.0\" \\\n", + " \"jsonschema-specifications==2025.9.1\" \\\n", + " \"keyring==25.7.0\" \\\n", + " \"keyrings-alt==5.0.2\" \\\n", + " \"kiwisolver==1.5.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"ml-dtypes==0.5.4\" \\\n", + " \"more-itertools==10.8.0\" \\\n", + " \"multidict==6.7.1\" \\\n", + " \"natsort==8.4.0\" \\\n", + " \"ndx-events==0.4.0\" \\\n", + " \"numcodecs==0.15.1\" \\\n", + " \"numpy==2.0.2\" \\\n", + " \"nwbinspector==0.6.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", + " \"platformdirs==4.9.6\" \\\n", + " \"propcache==0.4.1\" \\\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", + " \"pynwb==2.8.3\" \\\n", + " \"pyout==0.8.1\" \\\n", + " \"pyparsing==3.3.2\" \\\n", + " \"python-dateutil==2.9.0.post0\" \\\n", + " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", + " \"pyyaml==6.0.3\" \\\n", + " \"referencing==0.37.0\" \\\n", + " \"requests==2.32.4\" \\\n", + " \"rfc3339-validator==0.1.4\" \\\n", + " \"rfc3987==1.3.8\" \\\n", + " \"rpds-py==0.30.0\" \\\n", + " \"ruamel-yaml==0.19.1\" \\\n", + " \"secretstorage==3.5.0\" \\\n", + " \"semantic-version==2.10.0\" \\\n", + " \"six==1.17.0\" \\\n", + " \"tenacity==9.1.4\" \\\n", + " \"tensorstore==0.1.82\" \\\n", + " \"threadpoolctl==3.6.0\" \\\n", + " \"tqdm==4.67.3\" \\\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", + " \"wrapt==2.1.2\" \\\n", + " \"yarl==1.23.0\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", "\n", "!curl -sL -o stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000971/lernerlab/seiler_2024/stream_nwbfile.py" diff --git a/001038/DombeckLab/001038_demo.ipynb b/001038/DombeckLab/001038_demo.ipynb index 24c96ed..0c8da3e 100644 --- a/001038/DombeckLab/001038_demo.ipynb +++ b/001038/DombeckLab/001038_demo.ipynb @@ -33,122 +33,120 @@ "# 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", - " \"arrow==1.4.0\" \\\\\n", - " \"asciitree==0.3.3\" \\\\\n", - " \"asttokens==3.0.1\" \\\\\n", - " \"attrs==26.1.0\" \\\\\n", - " \"bids-validator-deno==2.4.1\" \\\\\n", - " \"bidsschematools==1.2.2\" \\\\\n", - " \"blessed==1.39.0\" \\\\\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==48.0.0\" \\\\\n", - " \"cycler==0.12.1\" \\\\\n", - " \"dandi==0.74.3\" \\\\\n", - " \"dandischema==0.12.1\" \\\\\n", - " \"decorator==5.2.1\" \\\\\n", - " \"deprecated==1.3.1\" \\\\\n", - " \"dnspython==2.8.0\" \\\\\n", - " \"email-validator==2.3.0\" \\\\\n", - " \"etelemetry==0.3.1\" \\\\\n", - " \"executing==2.2.1\" \\\\\n", - " \"fasteners==0.20\" \\\\\n", - " \"fonttools==4.62.1\" \\\\\n", - " \"fqdn==1.5.1\" \\\\\n", - " \"frozenlist==1.8.0\" \\\\\n", - " \"fscacher==0.4.4\" \\\\\n", - " \"fsspec==2026.4.0\" \\\\\n", - " \"h5py==3.16.0\" \\\\\n", - " \"hdmf==3.14.6\" \\\\\n", - " \"hdmf-zarr==0.11.3\" \\\\\n", - " \"humanize==4.15.0\" \\\\\n", - " \"idna==3.14\" \\\\\n", - " \"interleave==0.3.0\" \\\\\n", - " \"ipython==9.13.0\" \\\\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\\\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", - " \"joblib==1.5.3\" \\\\\n", - " \"jsonpointer==3.1.1\" \\\\\n", - " \"jsonschema==4.26.0\" \\\\\n", - " \"jsonschema-specifications==2025.9.1\" \\\\\n", - " \"keyring==25.7.0\" \\\\\n", - " \"keyrings-alt==5.0.2\" \\\\\n", - " \"kiwisolver==1.5.0\" \\\\\n", - " \"matplotlib==3.10.9\" \\\\\n", - " \"matplotlib-inline==0.2.2\" \\\\\n", - " \"ml-dtypes==0.5.4\" \\\\\n", - " \"more-itertools==11.0.2\" \\\\\n", - " \"multidict==6.7.1\" \\\\\n", - " \"natsort==8.4.0\" \\\\\n", - " \"numcodecs==0.15.1\" \\\\\n", - " \"numpy==2.4.4\" \\\\\n", - " \"nwbinspector==0.6.3\" \\\\\n", - " \"packaging==26.2\" \\\\\n", - " \"pandas==3.0.3\" \\\\\n", - " \"parso==0.8.7\" \\\\\n", - " \"pexpect==4.9.0\" \\\\\n", - " \"pillow==12.2.0\" \\\\\n", - " \"platformdirs==4.9.6\" \\\\\n", - " \"prompt-toolkit==3.0.52\" \\\\\n", - " \"propcache==0.5.2\" \\\\\n", - " \"psutil==7.2.2\" \\\\\n", - " \"ptyprocess==0.7.0\" \\\\\n", - " \"pure-eval==0.2.3\" \\\\\n", - " \"pycparser==3.0\" \\\\\n", - " \"pycryptodomex==3.23.0\" \\\\\n", - " \"pydantic==2.13.4\" \\\\\n", - " \"pydantic-core==2.46.4\" \\\\\n", - " \"pydantic-settings==2.14.1\" \\\\\n", - " \"pygments==2.20.0\" \\\\\n", - " \"pynwb==2.8.3\" \\\\\n", - " \"pyout==0.8.1\" \\\\\n", - " \"pyparsing==3.3.2\" \\\\\n", - " \"python-dateutil==2.9.0.post0\" \\\\\n", - " \"python-dotenv==1.2.2\" \\\\\n", - " \"pyyaml==6.0.3\" \\\\\n", - " \"referencing==0.37.0\" \\\\\n", - " \"remfile==0.1.13\" \\\\\n", - " \"requests==2.34.0\" \\\\\n", - " \"rfc3339-validator==0.1.4\" \\\\\n", - " \"rfc3987==1.3.8\" \\\\\n", - " \"rpds-py==0.30.0\" \\\\\n", - " \"ruamel-yaml==0.19.1\" \\\\\n", - " \"scipy==1.17.1\" \\\\\n", - " \"secretstorage==3.5.0\" \\\\\n", - " \"semantic-version==2.10.0\" \\\\\n", - " \"six==1.17.0\" \\\\\n", - " \"stack-data==0.6.3\" \\\\\n", - " \"tenacity==9.1.4\" \\\\\n", - " \"tensorstore==0.1.83\" \\\\\n", - " \"threadpoolctl==3.6.0\" \\\\\n", - " \"tqdm==4.67.3\" \\\\\n", - " \"traitlets==5.15.0\" \\\\\n", - " \"typing-extensions==4.15.0\" \\\\\n", - " \"typing-inspection==0.4.2\" \\\\\n", - " \"tzdata==2026.2\" \\\\\n", - " \"uri-template==1.3.0\" \\\\\n", - " \"urllib3==2.7.0\" \\\\\n", - " \"wcwidth==0.7.0\" \\\\\n", - " \"webcolors==25.10.0\" \\\\\n", - " \"wrapt==2.1.2\" \\\\\n", - " \"yarl==1.23.0\" \\\\\n", - " \"zarr==2.18.7\" \\\\\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", + " \"arrow==1.4.0\" \\\n", + " \"asciitree==0.3.3\" \\\n", + " \"asttokens==3.0.1\" \\\n", + " \"attrs==26.1.0\" \\\n", + " \"bids-validator-deno==2.4.1\" \\\n", + " \"bidsschematools==1.2.2\" \\\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==0.74.3\" \\\n", + " \"dandischema==0.12.1\" \\\n", + " \"decorator==4.4.2\" \\\n", + " \"deprecated==1.3.1\" \\\n", + " \"dnspython==2.8.0\" \\\n", + " \"email-validator==2.3.0\" \\\n", + " \"etelemetry==0.3.1\" \\\n", + " \"executing==2.2.1\" \\\n", + " \"fasteners==0.20\" \\\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==6.0.1\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", + " \"humanize==4.15.0\" \\\n", + " \"idna==3.13\" \\\n", + " \"interleave==0.3.0\" \\\n", + " \"ipython==8.21.0\" \\\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", + " \"joblib==1.5.3\" \\\n", + " \"jsonpointer==3.1.1\" \\\n", + " \"jsonschema==4.26.0\" \\\n", + " \"jsonschema-specifications==2025.9.1\" \\\n", + " \"keyring==25.7.0\" \\\n", + " \"keyrings-alt==5.0.2\" \\\n", + " \"kiwisolver==1.5.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", + " \"ml-dtypes==0.5.4\" \\\n", + " \"more-itertools==10.8.0\" \\\n", + " \"multidict==6.7.1\" \\\n", + " \"natsort==8.4.0\" \\\n", + " \"numcodecs==0.15.1\" \\\n", + " \"numpy==2.0.2\" \\\n", + " \"nwbinspector==0.6.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", + " \"pexpect==4.9.0\" \\\n", + " \"pillow==11.3.0\" \\\n", + " \"platformdirs==4.9.6\" \\\n", + " \"prompt-toolkit==3.0.52\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"ptyprocess==0.7.0\" \\\n", + " \"pure-eval==0.2.3\" \\\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==2.8.3\" \\\n", + " \"pyout==0.8.1\" \\\n", + " \"pyparsing==3.3.2\" \\\n", + " \"python-dateutil==2.9.0.post0\" \\\n", + " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", + " \"pyyaml==6.0.3\" \\\n", + " \"referencing==0.37.0\" \\\n", + " \"remfile==0.1.13\" \\\n", + " \"requests==2.32.4\" \\\n", + " \"rfc3339-validator==0.1.4\" \\\n", + " \"rfc3987==1.3.8\" \\\n", + " \"rpds-py==0.30.0\" \\\n", + " \"ruamel-yaml==0.19.1\" \\\n", + " \"secretstorage==3.5.0\" \\\n", + " \"semantic-version==2.10.0\" \\\n", + " \"six==1.17.0\" \\\n", + " \"stack-data==0.6.3\" \\\n", + " \"tenacity==9.1.4\" \\\n", + " \"tensorstore==0.1.82\" \\\n", + " \"threadpoolctl==3.6.0\" \\\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", + " \"wrapt==2.1.2\" \\\n", + " \"yarl==1.23.0\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] }, diff --git a/001075/001075_paper_figure_1d.ipynb b/001075/001075_paper_figure_1d.ipynb index e896683..773e7a5 100644 --- a/001075/001075_paper_figure_1d.ipynb +++ b/001075/001075_paper_figure_1d.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,51 +84,52 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/001084/HoweLab/001084_demo.ipynb b/001084/HoweLab/001084_demo.ipynb index 293ac17..1e9f553 100644 --- a/001084/HoweLab/001084_demo.ipynb +++ b/001084/HoweLab/001084_demo.ipynb @@ -33,106 +33,106 @@ "# 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", - " \"arrow==1.4.0\" \\\\\n", - " \"asciitree==0.3.3\" \\\\\n", - " \"attrs==26.1.0\" \\\\\n", - " \"bids-validator-deno==2.4.1\" \\\\\n", - " \"bidsschematools==1.2.2\" \\\\\n", - " \"blessed==1.39.0\" \\\\\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==48.0.0\" \\\\\n", - " \"cycler==0.12.1\" \\\\\n", - " \"dandi==0.74.3\" \\\\\n", - " \"dandischema==0.12.1\" \\\\\n", - " \"deprecated==1.3.1\" \\\\\n", - " \"dnspython==2.8.0\" \\\\\n", - " \"email-validator==2.3.0\" \\\\\n", - " \"etelemetry==0.3.1\" \\\\\n", - " \"fasteners==0.20\" \\\\\n", - " \"fonttools==4.62.1\" \\\\\n", - " \"fqdn==1.5.1\" \\\\\n", - " \"frozenlist==1.8.0\" \\\\\n", - " \"fscacher==0.4.4\" \\\\\n", - " \"fsspec==2026.4.0\" \\\\\n", - " \"h5py==3.16.0\" \\\\\n", - " \"hdmf==3.14.6\" \\\\\n", - " \"hdmf-zarr==0.11.3\" \\\\\n", - " \"humanize==4.15.0\" \\\\\n", - " \"idna==3.14\" \\\\\n", - " \"interleave==0.3.0\" \\\\\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", - " \"jeepney==0.9.0\" \\\\\n", - " \"joblib==1.5.3\" \\\\\n", - " \"jsonpointer==3.1.1\" \\\\\n", - " \"jsonschema==4.26.0\" \\\\\n", - " \"jsonschema-specifications==2025.9.1\" \\\\\n", - " \"keyring==25.7.0\" \\\\\n", - " \"keyrings-alt==5.0.2\" \\\\\n", - " \"kiwisolver==1.5.0\" \\\\\n", - " \"matplotlib==3.10.9\" \\\\\n", - " \"ml-dtypes==0.5.4\" \\\\\n", - " \"more-itertools==11.0.2\" \\\\\n", - " \"multidict==6.7.1\" \\\\\n", - " \"natsort==8.4.0\" \\\\\n", - " \"numcodecs==0.15.1\" \\\\\n", - " \"numpy==2.4.4\" \\\\\n", - " \"nwbinspector==0.6.3\" \\\\\n", - " \"packaging==26.2\" \\\\\n", - " \"pandas==3.0.3\" \\\\\n", - " \"pillow==12.2.0\" \\\\\n", - " \"platformdirs==4.9.6\" \\\\\n", - " \"propcache==0.5.2\" \\\\\n", - " \"pycparser==3.0\" \\\\\n", - " \"pycryptodomex==3.23.0\" \\\\\n", - " \"pydantic==2.13.4\" \\\\\n", - " \"pydantic-core==2.46.4\" \\\\\n", - " \"pydantic-settings==2.14.1\" \\\\\n", - " \"pynwb==2.8.3\" \\\\\n", - " \"pyout==0.8.1\" \\\\\n", - " \"pyparsing==3.3.2\" \\\\\n", - " \"python-dateutil==2.9.0.post0\" \\\\\n", - " \"python-dotenv==1.2.2\" \\\\\n", - " \"pyyaml==6.0.3\" \\\\\n", - " \"referencing==0.37.0\" \\\\\n", - " \"remfile==0.1.13\" \\\\\n", - " \"requests==2.34.0\" \\\\\n", - " \"rfc3339-validator==0.1.4\" \\\\\n", - " \"rfc3987==1.3.8\" \\\\\n", - " \"rpds-py==0.30.0\" \\\\\n", - " \"ruamel-yaml==0.19.1\" \\\\\n", - " \"scipy==1.17.1\" \\\\\n", - " \"secretstorage==3.5.0\" \\\\\n", - " \"semantic-version==2.10.0\" \\\\\n", - " \"six==1.17.0\" \\\\\n", - " \"tenacity==9.1.4\" \\\\\n", - " \"tensorstore==0.1.83\" \\\\\n", - " \"threadpoolctl==3.6.0\" \\\\\n", - " \"tqdm==4.67.3\" \\\\\n", - " \"typing-extensions==4.15.0\" \\\\\n", - " \"typing-inspection==0.4.2\" \\\\\n", - " \"tzdata==2026.2\" \\\\\n", - " \"uri-template==1.3.0\" \\\\\n", - " \"urllib3==2.7.0\" \\\\\n", - " \"wcwidth==0.7.0\" \\\\\n", - " \"webcolors==25.10.0\" \\\\\n", - " \"wrapt==2.1.2\" \\\\\n", - " \"yarl==1.23.0\" \\\\\n", - " \"zarr==2.18.7\" \\\\\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", + " \"arrow==1.4.0\" \\\n", + " \"asciitree==0.3.3\" \\\n", + " \"attrs==26.1.0\" \\\n", + " \"bids-validator-deno==2.4.1\" \\\n", + " \"bidsschematools==1.2.2\" \\\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==0.74.3\" \\\n", + " \"dandischema==0.12.1\" \\\n", + " \"deprecated==1.3.1\" \\\n", + " \"dnspython==2.8.0\" \\\n", + " \"email-validator==2.3.0\" \\\n", + " \"etelemetry==0.3.1\" \\\n", + " \"fasteners==0.20\" \\\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==6.0.1\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", + " \"humanize==4.15.0\" \\\n", + " \"idna==3.13\" \\\n", + " \"interleave==0.3.0\" \\\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", + " \"jeepney==0.9.0\" \\\n", + " \"joblib==1.5.3\" \\\n", + " \"jsonpointer==3.1.1\" \\\n", + " \"jsonschema==4.26.0\" \\\n", + " \"jsonschema-specifications==2025.9.1\" \\\n", + " \"keyring==25.7.0\" \\\n", + " \"keyrings-alt==5.0.2\" \\\n", + " \"kiwisolver==1.5.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"ml-dtypes==0.5.4\" \\\n", + " \"more-itertools==10.8.0\" \\\n", + " \"multidict==6.7.1\" \\\n", + " \"natsort==8.4.0\" \\\n", + " \"numcodecs==0.15.1\" \\\n", + " \"numpy==2.0.2\" \\\n", + " \"nwbinspector==0.6.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", + " \"platformdirs==4.9.6\" \\\n", + " \"propcache==0.4.1\" \\\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", + " \"pynwb==2.8.3\" \\\n", + " \"pyout==0.8.1\" \\\n", + " \"pyparsing==3.3.2\" \\\n", + " \"python-dateutil==2.9.0.post0\" \\\n", + " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", + " \"pyyaml==6.0.3\" \\\n", + " \"referencing==0.37.0\" \\\n", + " \"remfile==0.1.13\" \\\n", + " \"requests==2.32.4\" \\\n", + " \"rfc3339-validator==0.1.4\" \\\n", + " \"rfc3987==1.3.8\" \\\n", + " \"rpds-py==0.30.0\" \\\n", + " \"ruamel-yaml==0.19.1\" \\\n", + " \"secretstorage==3.5.0\" \\\n", + " \"semantic-version==2.10.0\" \\\n", + " \"six==1.17.0\" \\\n", + " \"tenacity==9.1.4\" \\\n", + " \"tensorstore==0.1.82\" \\\n", + " \"threadpoolctl==3.6.0\" \\\n", + " \"tqdm==4.67.3\" \\\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", + " \"wrapt==2.1.2\" \\\n", + " \"yarl==1.23.0\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] }, diff --git a/001172/HigleyLab/001172_demo.ipynb b/001172/HigleyLab/001172_demo.ipynb index ac399a0..90f4801 100644 --- a/001172/HigleyLab/001172_demo.ipynb +++ b/001172/HigleyLab/001172_demo.ipynb @@ -43,42 +43,41 @@ " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\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", - " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", @@ -86,12 +85,12 @@ " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.15\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", - " \"ipywidgets==8.1.8\" \\\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", @@ -106,12 +105,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -122,40 +121,42 @@ " \"kiwisolver==1.5.0\" \\\n", " \"lark==1.3.1\" \\\n", " \"markupsafe==3.0.3\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", - " \"mistune==3.2.1\" \\\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==11.0.2\" \\\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", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -163,43 +164,43 @@ " \"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==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\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==4.0.15\" \\\n", + " \"widgetsnbextension==3.6.10\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", " \"zarr==2.18.7\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb index 38a1e15..512d9f8 100644 --- a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb +++ b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb @@ -33,7 +33,7 @@ "# pinned below so the notebook is reproducible regardless of resolver drift.\n", "!pip install -q uv\n", "!uv pip install --system \\\n", - " \"absl-py==2.4.0\" \\\n", + " \"absl-py==1.4.0\" \\\n", " \"acres==0.5.0\" \\\n", " \"aiohappyeyeballs==2.6.1\" \\\n", " \"aiohttp==3.13.5\" \\\n", @@ -43,15 +43,16 @@ " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", - " \"asttokens==3.0.1\" \\\n", + " \"asciitree==0.3.3\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -60,40 +61,38 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dandi==0.74.3\" \\\n", + " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"donfig==0.8.1.post1\" \\\n", " \"email-validator==2.3.0\" \\\n", + " \"entrypoints==0.4\" \\\n", " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.15.1\" \\\n", " \"hdmf==4.3.1\" \\\n", - " \"hdmf-zarr==0.6.0\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipykernel==6.17.1\" \\\n", + " \"ipython==7.34.0\" \\\n", + " \"ipython-genutils==0.2.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -112,12 +111,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -129,22 +128,23 @@ " \"lark==1.3.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.8\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"mdurl==0.1.2\" \\\n", - " \"mistune==3.2.1\" \\\n", + " \"mistune==3.2.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\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", " \"nemos==0.2.6\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -153,24 +153,25 @@ " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", " \"optimistix==0.0.11\" \\\n", - " \"packaging==26.2\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", " \"pandas==2.3.3\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -179,52 +180,51 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"python-json-logger==4.1.0\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", - " \"pyzmq==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-learn==1.8.0\" \\\n", + " \"scikit-learn==1.6.1\" \\\n", " \"scipy==1.15.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.5.1\" \\\n", " \"websocket-client==1.9.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", - " \"xarray==2026.4.0\" \\\n", + " \"xarray==2025.12.0\" \\\n", " \"yarl==1.23.0\" \\\n", - " \"zarr==3.1.5\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", "\n", "!curl -sL -o notebook_helpers.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001636/TurnerLab/motor_cortex/notebook_helpers.py" diff --git a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb index b3f587b..dccf9d9 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb @@ -33,7 +33,7 @@ "# pinned below so the notebook is reproducible regardless of resolver drift.\n", "!pip install -q uv\n", "!uv pip install --system \\\n", - " \"absl-py==2.4.0\" \\\n", + " \"absl-py==1.4.0\" \\\n", " \"acres==0.5.0\" \\\n", " \"aiohappyeyeballs==2.6.1\" \\\n", " \"aiohttp==3.13.5\" \\\n", @@ -43,15 +43,16 @@ " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", - " \"asttokens==3.0.1\" \\\n", + " \"asciitree==0.3.3\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -60,40 +61,38 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dandi==0.74.3\" \\\n", + " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"donfig==0.8.1.post1\" \\\n", " \"email-validator==2.3.0\" \\\n", + " \"entrypoints==0.4\" \\\n", " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.15.1\" \\\n", " \"hdmf==4.3.1\" \\\n", - " \"hdmf-zarr==0.6.0\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipykernel==6.17.1\" \\\n", + " \"ipython==7.34.0\" \\\n", + " \"ipython-genutils==0.2.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -112,12 +111,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -129,22 +128,23 @@ " \"lark==1.3.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.8\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"mdurl==0.1.2\" \\\n", - " \"mistune==3.2.1\" \\\n", + " \"mistune==3.2.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\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", " \"nemos==0.2.6\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -153,24 +153,25 @@ " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", " \"optimistix==0.0.11\" \\\n", - " \"packaging==26.2\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", " \"pandas==2.3.3\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -179,52 +180,51 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"python-json-logger==4.1.0\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", - " \"pyzmq==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-learn==1.8.0\" \\\n", + " \"scikit-learn==1.6.1\" \\\n", " \"scipy==1.15.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.5.1\" \\\n", " \"websocket-client==1.9.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", - " \"xarray==2026.4.0\" \\\n", + " \"xarray==2025.12.0\" \\\n", " \"yarl==1.23.0\" \\\n", - " \"zarr==3.1.5\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] }, diff --git a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb index 1a156a3..683f71a 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb @@ -33,7 +33,7 @@ "# pinned below so the notebook is reproducible regardless of resolver drift.\n", "!pip install -q uv\n", "!uv pip install --system \\\n", - " \"absl-py==2.4.0\" \\\n", + " \"absl-py==1.4.0\" \\\n", " \"acres==0.5.0\" \\\n", " \"aiohappyeyeballs==2.6.1\" \\\n", " \"aiohttp==3.13.5\" \\\n", @@ -43,15 +43,16 @@ " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", - " \"asttokens==3.0.1\" \\\n", + " \"asciitree==0.3.3\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -60,40 +61,38 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dandi==0.74.3\" \\\n", + " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"donfig==0.8.1.post1\" \\\n", " \"email-validator==2.3.0\" \\\n", + " \"entrypoints==0.4\" \\\n", " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.15.1\" \\\n", " \"hdmf==4.3.1\" \\\n", - " \"hdmf-zarr==0.6.0\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipykernel==6.17.1\" \\\n", + " \"ipython==7.34.0\" \\\n", + " \"ipython-genutils==0.2.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -112,12 +111,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -129,22 +128,23 @@ " \"lark==1.3.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.8\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"mdurl==0.1.2\" \\\n", - " \"mistune==3.2.1\" \\\n", + " \"mistune==3.2.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\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", " \"nemos==0.2.6\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -153,24 +153,25 @@ " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", " \"optimistix==0.0.11\" \\\n", - " \"packaging==26.2\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", " \"pandas==2.3.3\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -179,52 +180,51 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"python-json-logger==4.1.0\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", - " \"pyzmq==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-learn==1.8.0\" \\\n", + " \"scikit-learn==1.6.1\" \\\n", " \"scipy==1.15.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.5.1\" \\\n", " \"websocket-client==1.9.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", - " \"xarray==2026.4.0\" \\\n", + " \"xarray==2025.12.0\" \\\n", " \"yarl==1.23.0\" \\\n", - " \"zarr==3.1.5\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] }, diff --git a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb index 43d0d95..c2c5dbf 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb @@ -33,7 +33,7 @@ "# pinned below so the notebook is reproducible regardless of resolver drift.\n", "!pip install -q uv\n", "!uv pip install --system \\\n", - " \"absl-py==2.4.0\" \\\n", + " \"absl-py==1.4.0\" \\\n", " \"acres==0.5.0\" \\\n", " \"aiohappyeyeballs==2.6.1\" \\\n", " \"aiohttp==3.13.5\" \\\n", @@ -43,15 +43,16 @@ " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==25.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", - " \"asttokens==3.0.1\" \\\n", + " \"asciitree==0.3.3\" \\\n", " \"async-lru==2.3.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"babel==2.18.0\" \\\n", - " \"beautifulsoup4==4.14.3\" \\\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==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -60,40 +61,38 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dandi==0.74.3\" \\\n", + " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"debugpy==1.8.20\" \\\n", - " \"decorator==5.2.1\" \\\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", - " \"donfig==0.8.1.post1\" \\\n", " \"email-validator==2.3.0\" \\\n", + " \"entrypoints==0.4\" \\\n", " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\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==2026.4.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h11==0.16.0\" \\\n", " \"h5py==3.15.1\" \\\n", " \"hdmf==4.3.1\" \\\n", - " \"hdmf-zarr==0.6.0\" \\\n", + " \"hdmf-zarr==0.12.0\" \\\n", " \"httpcore==1.0.9\" \\\n", " \"httpx==0.28.1\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipykernel==7.2.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipykernel==6.17.1\" \\\n", + " \"ipython==7.34.0\" \\\n", + " \"ipython-genutils==0.2.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -112,12 +111,12 @@ " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"jupyter==1.1.1\" \\\n", - " \"jupyter-client==8.8.0\" \\\n", + " \"jupyter-client==7.4.9\" \\\n", " \"jupyter-console==6.6.3\" \\\n", " \"jupyter-core==5.9.1\" \\\n", " \"jupyter-events==0.12.1\" \\\n", " \"jupyter-lsp==2.3.1\" \\\n", - " \"jupyter-server==2.18.2\" \\\n", + " \"jupyter-server==2.14.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab==4.5.7\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", @@ -129,22 +128,23 @@ " \"lark==1.3.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.8\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"mdurl==0.1.2\" \\\n", - " \"mistune==3.2.1\" \\\n", + " \"mistune==3.2.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\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", " \"nemos==0.2.6\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"notebook==7.5.6\" \\\n", + " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -153,24 +153,25 @@ " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", " \"optimistix==0.0.11\" \\\n", - " \"packaging==26.2\" \\\n", + " \"overrides==7.7.0\" \\\n", + " \"packaging==26.1\" \\\n", " \"pandas==2.3.3\" \\\n", " \"pandocfilters==1.5.1\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\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==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", + " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -179,52 +180,51 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"python-json-logger==4.1.0\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", - " \"pyzmq==27.1.0\" \\\n", + " \"pyzmq==26.2.1\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\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", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-learn==1.8.0\" \\\n", + " \"scikit-learn==1.6.1\" \\\n", " \"scipy==1.15.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==82.0.1\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.8.3\" \\\n", - " \"stack-data==0.6.3\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"terminado==0.18.1\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tinycss2==1.4.0\" \\\n", - " \"tornado==6.5.5\" \\\n", + " \"tornado==6.5.1\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.5.1\" \\\n", " \"websocket-client==1.9.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", - " \"xarray==2026.4.0\" \\\n", + " \"xarray==2025.12.0\" \\\n", " \"yarl==1.23.0\" \\\n", - " \"zarr==3.1.5\" \\\n", + " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", "\n", "!curl -sL -o trial_structure_plot.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001636/TurnerLab/motor_cortex/trial_structure_plot.py" @@ -242,6 +242,7 @@ }, { "cell_type": "markdown", + "id": "e44e8253", "metadata": {}, "source": [ "# Turner Lab M1 MPTP Dataset - NWB Usage Guide\n", @@ -264,6 +265,7 @@ }, { "cell_type": "markdown", + "id": "86af34af", "metadata": {}, "source": [ "## Streaming NWB Files from DANDI \n", @@ -274,6 +276,7 @@ { "cell_type": "code", "execution_count": 1, + "id": "dca4d940", "metadata": {}, "outputs": [ { @@ -330,6 +333,7 @@ }, { "cell_type": "markdown", + "id": "c77309aa", "metadata": {}, "source": [ "Fist, we can visualize the HTML representation of the nwbfile to get an overview of its contents." @@ -338,6 +342,7 @@ { "cell_type": "code", "execution_count": 2, + "id": "a598f808", "metadata": {}, "outputs": [ { @@ -1400,6 +1405,7 @@ }, { "cell_type": "markdown", + "id": "0adfa768", "metadata": {}, "source": [ "## Understanding the Trial Structure\n", @@ -1410,6 +1416,7 @@ { "cell_type": "code", "execution_count": 3, + "id": "62b1b47b", "metadata": {}, "outputs": [ { @@ -1630,6 +1637,7 @@ }, { "cell_type": "markdown", + "id": "67f83a04", "metadata": {}, "source": [ "Trials are stored as a table in NWB. We can convert it to a pandas DataFrame to explore the structure of the trial events" @@ -1638,6 +1646,7 @@ { "cell_type": "code", "execution_count": 4, + "id": "b20c259d", "metadata": {}, "outputs": [ { @@ -1890,6 +1899,7 @@ }, { "cell_type": "markdown", + "id": "aa86cc8a", "metadata": {}, "source": [ "### Trial Event Sequence\n", @@ -1900,6 +1910,7 @@ { "cell_type": "code", "execution_count": 5, + "id": "27f1c947", "metadata": {}, "outputs": [ { @@ -2027,6 +2038,7 @@ }, { "cell_type": "markdown", + "id": "ce816ed8", "metadata": {}, "source": [ "Each trial progresses through distinct phases:\n", @@ -2047,6 +2059,7 @@ { "cell_type": "code", "execution_count": 6, + "id": "3cc51c50", "metadata": {}, "outputs": [ { @@ -2068,6 +2081,7 @@ }, { "cell_type": "markdown", + "id": "0aae5c33", "metadata": {}, "source": [ "The visualization above shows the temporal structure of individual trials as horizontal stacked bars. Each row represents one trial, with colored segments indicating different task phases:\n", @@ -2084,6 +2098,7 @@ }, { "cell_type": "markdown", + "id": "96c10f8e", "metadata": {}, "source": [ "### Derived Kinematic Measures\n", @@ -2109,6 +2124,7 @@ { "cell_type": "code", "execution_count": 7, + "id": "f6d7be09", "metadata": {}, "outputs": [ { @@ -2254,6 +2270,7 @@ { "cell_type": "code", "execution_count": 8, + "id": "898d7b68", "metadata": {}, "outputs": [ { @@ -2293,6 +2310,7 @@ }, { "cell_type": "markdown", + "id": "41f0fe5c", "metadata": {}, "source": [ "### Torque Perturbation Trials\n", @@ -2318,6 +2336,7 @@ { "cell_type": "code", "execution_count": 9, + "id": "d2a8f299", "metadata": {}, "outputs": [ { @@ -2446,6 +2465,7 @@ { "cell_type": "code", "execution_count": 10, + "id": "32e03705", "metadata": {}, "outputs": [ { @@ -2493,6 +2513,7 @@ }, { "cell_type": "markdown", + "id": "386ac7dc", "metadata": {}, "source": [ "### Isolation Monitoring Stimulation\n", @@ -2518,6 +2539,7 @@ { "cell_type": "code", "execution_count": 11, + "id": "781c03bd", "metadata": {}, "outputs": [ { @@ -2578,6 +2600,7 @@ { "cell_type": "code", "execution_count": 12, + "id": "a5f316b7", "metadata": {}, "outputs": [ { @@ -2618,6 +2641,7 @@ }, { "cell_type": "markdown", + "id": "b3c0e818", "metadata": {}, "source": [ "## Accessing Neurons/Units Spikes\n", @@ -2628,6 +2652,7 @@ { "cell_type": "code", "execution_count": 13, + "id": "9668027c", "metadata": {}, "outputs": [ { @@ -2787,6 +2812,7 @@ }, { "cell_type": "markdown", + "id": "99e9c5ba", "metadata": {}, "source": [ "Like the trials table, the units table is a DynamicTable that can be converted to a pandas DataFrame for easier exploration and analysis." @@ -2795,6 +2821,7 @@ { "cell_type": "code", "execution_count": 14, + "id": "dc566df8", "metadata": {}, "outputs": [ { @@ -2943,6 +2970,7 @@ }, { "cell_type": "markdown", + "id": "233c50cd", "metadata": {}, "source": [ "### Accessing Spike Times\n", @@ -2953,6 +2981,7 @@ { "cell_type": "code", "execution_count": 15, + "id": "f4fa306d", "metadata": {}, "outputs": [ { @@ -2987,6 +3016,7 @@ { "cell_type": "code", "execution_count": 16, + "id": "822b2900", "metadata": {}, "outputs": [ { @@ -3024,6 +3054,7 @@ }, { "cell_type": "markdown", + "id": "8b4d9f66", "metadata": {}, "source": [ "### Understanding Observation Intervals (Trialized Data)\n", @@ -3038,6 +3069,7 @@ { "cell_type": "code", "execution_count": 17, + "id": "91cde777", "metadata": {}, "outputs": [ { @@ -3099,6 +3131,7 @@ }, { "cell_type": "markdown", + "id": "a37348f5", "metadata": {}, "source": [ "Each unit has an `obs_intervals` column that specifies exactly when it was being recorded (i.e., during trials only). This is critical for accurate analysis:\n", @@ -3109,6 +3142,7 @@ { "cell_type": "code", "execution_count": 18, + "id": "f82884fe", "metadata": {}, "outputs": [ { @@ -3153,6 +3187,7 @@ }, { "cell_type": "markdown", + "id": "856bf1ac", "metadata": {}, "source": [ "### Invalid Times Table (For Continuous Signals)\n", @@ -3170,6 +3205,7 @@ { "cell_type": "code", "execution_count": 19, + "id": "91c47cce", "metadata": {}, "outputs": [ { @@ -3262,6 +3298,7 @@ }, { "cell_type": "markdown", + "id": "70fe6f17", "metadata": {}, "source": [ "### Neuron Projection Type (Cell Classification)\n", @@ -3286,6 +3323,7 @@ { "cell_type": "code", "execution_count": 20, + "id": "73a7f932", "metadata": {}, "outputs": [ { @@ -3357,6 +3395,7 @@ }, { "cell_type": "markdown", + "id": "0fe81b90", "metadata": {}, "source": [ "### Antidromic Identification Parameters\n", @@ -3379,6 +3418,7 @@ { "cell_type": "code", "execution_count": 21, + "id": "46e004ed", "metadata": {}, "outputs": [ { @@ -3464,6 +3504,7 @@ }, { "cell_type": "markdown", + "id": "8a98b205", "metadata": {}, "source": [ "### Receptive Field Properties\n", @@ -3490,6 +3531,7 @@ { "cell_type": "code", "execution_count": 22, + "id": "5fea89bc", "metadata": {}, "outputs": [ { @@ -3562,6 +3604,7 @@ { "cell_type": "code", "execution_count": 23, + "id": "3ff22a9b", "metadata": {}, "outputs": [ { @@ -3648,6 +3691,7 @@ }, { "cell_type": "markdown", + "id": "c14eccb2", "metadata": {}, "source": [ "### Additional Unit Metadata\n", @@ -3662,6 +3706,7 @@ }, { "cell_type": "markdown", + "id": "f73289f8", "metadata": {}, "source": [ "### Electrodes Table\n", @@ -3684,6 +3729,7 @@ { "cell_type": "code", "execution_count": 24, + "id": "f62def97", "metadata": {}, "outputs": [ { @@ -3799,6 +3845,7 @@ { "cell_type": "code", "execution_count": 25, + "id": "522d76c4", "metadata": {}, "outputs": [ { @@ -3824,6 +3871,7 @@ }, { "cell_type": "markdown", + "id": "38c24d5c", "metadata": {}, "source": [ "## Analog Signals (Kinematics, EMG, LFP)\n", @@ -3834,6 +3882,7 @@ { "cell_type": "code", "execution_count": 26, + "id": "7761c893", "metadata": {}, "outputs": [ { @@ -4208,6 +4257,7 @@ }, { "cell_type": "markdown", + "id": "78207e9c", "metadata": {}, "source": [ "### Manipulandum Signals (Kinematics)\n", @@ -4228,6 +4278,7 @@ { "cell_type": "code", "execution_count": 27, + "id": "a8dfae3b", "metadata": {}, "outputs": [ { @@ -4259,6 +4310,7 @@ { "cell_type": "code", "execution_count": 28, + "id": "f55b4621", "metadata": {}, "outputs": [ { @@ -4303,6 +4355,7 @@ }, { "cell_type": "markdown", + "id": "ebe50645", "metadata": {}, "source": [ "### EMG Signals\n", @@ -4315,6 +4368,7 @@ { "cell_type": "code", "execution_count": 29, + "id": "7443edc4", "metadata": {}, "outputs": [ { @@ -4346,6 +4400,7 @@ { "cell_type": "code", "execution_count": 30, + "id": "d6a930d8", "metadata": {}, "outputs": [ { @@ -4388,6 +4443,7 @@ }, { "cell_type": "markdown", + "id": "41438991", "metadata": {}, "source": [ "### LFP Signal\n", @@ -4400,6 +4456,7 @@ { "cell_type": "code", "execution_count": 31, + "id": "56514060", "metadata": {}, "outputs": [ { @@ -4455,6 +4512,7 @@ }, { "cell_type": "markdown", + "id": "92e9d83b", "metadata": {}, "source": [ "## Antidromic Stimulation Raw Waveforms\n", @@ -4484,6 +4542,7 @@ { "cell_type": "code", "execution_count": 32, + "id": "9f80e4c9", "metadata": {}, "outputs": [ { @@ -4521,6 +4580,7 @@ { "cell_type": "code", "execution_count": 33, + "id": "cf3817a7", "metadata": {}, "outputs": [], "source": [ @@ -4533,6 +4593,7 @@ }, { "cell_type": "markdown", + "id": "f4e11e45", "metadata": {}, "source": [ "### Accessing Raw Antidromic Waveforms\n", @@ -4547,6 +4608,7 @@ { "cell_type": "code", "execution_count": 34, + "id": "6d7e5b46", "metadata": {}, "outputs": [ { @@ -4622,6 +4684,7 @@ { "cell_type": "code", "execution_count": 35, + "id": "bafd63d0", "metadata": {}, "outputs": [ { @@ -4685,6 +4748,7 @@ }, { "cell_type": "markdown", + "id": "afc04ad4", "metadata": {}, "source": [ "### Stimulation Electrodes Table\n", @@ -4703,6 +4767,7 @@ { "cell_type": "code", "execution_count": 36, + "id": "c33fea1a", "metadata": {}, "outputs": [ { @@ -4818,6 +4883,7 @@ { "cell_type": "code", "execution_count": null, + "id": "2f90d1a5", "metadata": {}, "outputs": [], "source": [] diff --git a/001754/CatalystNeuro/001754_demo.ipynb b/001754/CatalystNeuro/001754_demo.ipynb index eef8b26..c1e0cbd 100644 --- a/001754/CatalystNeuro/001754_demo.ipynb +++ b/001754/CatalystNeuro/001754_demo.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,28 +84,28 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"llvmlite==0.43.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"numba==0.65.1\" \\\n", + " \"numba==0.60.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.7.1\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -113,31 +113,31 @@ " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/dandi/DANDI User Guide, Part I.ipynb b/dandi/DANDI User Guide, Part I.ipynb index 8a54ce9..dffa6ef 100644 --- a/dandi/DANDI User Guide, Part I.ipynb +++ b/dandi/DANDI User Guide, Part I.ipynb @@ -40,13 +40,12 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", - " \"bqplot==0.13.1\" \\\n", - " \"bqscales==0.3.7\" \\\n", + " \"blessed==1.38.0\" \\\n", + " \"bqplot==0.12.45\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -55,28 +54,27 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fonttools==4.62.1\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"gast==0.7.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"imageio==2.37.3\" \\\n", " \"importlib-metadata==4.13.0\" \\\n", " \"interleave==0.3.0\" \\\n", @@ -84,9 +82,8 @@ " \"ipydatawidgets==4.3.2\" \\\n", " \"ipyfilechooser==0.6.0\" \\\n", " \"ipympl==0.10.0\" \\\n", - " \"ipython==9.13.0\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipython-genutils==0.2.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", " \"ipyvolume==0.6.3\" \\\n", " \"ipyvue==1.12.0\" \\\n", " \"ipyvuetify==1.11.3\" \\\n", @@ -108,10 +105,10 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"lazy-loader==0.5\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-grayscalevolume==0.0.2\" \\\n", @@ -119,27 +116,26 @@ " \"ndx-spectrum==0.2.2\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", " \"nwbwidgets==0.11.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"plotly==5.13.1\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"py2vega==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -147,33 +143,34 @@ " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", " \"pythreejs==2.4.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-image==0.26.0\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scikit-image==0.25.2\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", - " \"tifffile==2026.5.2\" \\\n", + " \"tifffile==2026.4.11\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"traittypes==0.2.3\" \\\n", " \"trimesh==4.12.2\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", diff --git a/dandi/DANDI User Guide, Part II.ipynb b/dandi/DANDI User Guide, Part II.ipynb index 1ea0e0e..4d918bb 100644 --- a/dandi/DANDI User Guide, Part II.ipynb +++ b/dandi/DANDI User Guide, Part II.ipynb @@ -43,14 +43,14 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\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", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", " \"deprecated==1.3.1\" \\\n", @@ -61,12 +61,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -81,29 +81,29 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", @@ -112,15 +112,15 @@ " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/demos/NWBWidget-demo.ipynb b/demos/NWBWidget-demo.ipynb index 85d23ab..c43f0c7 100644 --- a/demos/NWBWidget-demo.ipynb +++ b/demos/NWBWidget-demo.ipynb @@ -40,43 +40,40 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", - " \"bids-validator-deno==2.4.1\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", - " \"bqplot==0.13.1\" \\\n", - " \"bqscales==0.3.7\" \\\n", + " \"blessed==1.38.0\" \\\n", + " \"bqplot==0.12.45\" \\\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==8.3.3\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dandi==0.74.3\" \\\n", - " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"dandi==0.68.1\" \\\n", + " \"dandischema==0.11.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fonttools==4.62.1\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"gast==0.7.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"imageio==2.37.3\" \\\n", " \"importlib-metadata==4.13.0\" \\\n", " \"interleave==0.3.0\" \\\n", @@ -84,9 +81,8 @@ " \"ipydatawidgets==4.3.2\" \\\n", " \"ipyfilechooser==0.6.0\" \\\n", " \"ipympl==0.10.0\" \\\n", - " \"ipython==9.13.0\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipython-genutils==0.2.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", " \"ipyvolume==0.6.3\" \\\n", " \"ipyvue==1.12.0\" \\\n", " \"ipyvuetify==1.11.3\" \\\n", @@ -108,10 +104,10 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", " \"lazy-loader==0.5\" \\\n", - " \"matplotlib==3.10.9\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib==3.10.0\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-grayscalevolume==0.0.2\" \\\n", @@ -119,61 +115,59 @@ " \"ndx-spectrum==0.2.2\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", " \"nwbwidgets==0.11.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"plotly==5.13.1\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"py2vega==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", - " \"python-dotenv==1.2.2\" \\\n", " \"pythreejs==2.4.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scikit-image==0.26.0\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scikit-image==0.25.2\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", - " \"tifffile==2026.5.2\" \\\n", + " \"tifffile==2026.4.11\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"traittypes==0.2.3\" \\\n", " \"trimesh==4.12.2\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", @@ -195,6 +189,7 @@ }, { "cell_type": "markdown", + "id": "09f0b9f0", "metadata": {}, "source": [ "## NWB Widgets\n", @@ -209,6 +204,7 @@ { "cell_type": "code", "execution_count": null, + "id": "32a50677", "metadata": {}, "outputs": [], "source": [ @@ -249,6 +245,7 @@ { "cell_type": "code", "execution_count": null, + "id": "614cdb0d", "metadata": {}, "outputs": [], "source": [ @@ -263,6 +260,7 @@ }, { "cell_type": "markdown", + "id": "c9a33ed6", "metadata": {}, "source": [ "Note that these NWB files are quite large. In fact, we have chosen NWB files that contain raw data to demonstrate how data streaming can efficiently deal with these large files. Streaming works efficiently with NWB Widgets so that only the data necessary to create each view is read from DANDI. As a result, data transfer is minimized and data can be explored efficiently." @@ -271,6 +269,7 @@ { "cell_type": "code", "execution_count": null, + "id": "245802b3", "metadata": {}, "outputs": [], "source": [ @@ -283,6 +282,7 @@ }, { "cell_type": "markdown", + "id": "1b55a9bf", "metadata": {}, "source": [ "## Running NWBWidgets locally\n", @@ -293,6 +293,7 @@ { "cell_type": "code", "execution_count": null, + "id": "4d42dba5", "metadata": {}, "outputs": [], "source": [ @@ -304,6 +305,7 @@ }, { "cell_type": "markdown", + "id": "39565072", "metadata": {}, "source": [ "click the link that is output above ^^" @@ -312,6 +314,7 @@ { "cell_type": "code", "execution_count": null, + "id": "532a0f5b", "metadata": {}, "outputs": [], "source": [ @@ -324,6 +327,7 @@ }, { "cell_type": "markdown", + "id": "da6f34b0", "metadata": {}, "source": [ "When running with local data, NWBWidgets still only reads the data that is necessary from disk." diff --git a/tutorials/bcm_2024/analysis-demo.ipynb b/tutorials/bcm_2024/analysis-demo.ipynb index 52ab9e1..d48f3d2 100644 --- a/tutorials/bcm_2024/analysis-demo.ipynb +++ b/tutorials/bcm_2024/analysis-demo.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,28 +84,28 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"llvmlite==0.47.0\" \\\n", - " \"markdown-it-py==4.2.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"llvmlite==0.43.0\" \\\n", + " \"markdown-it-py==4.0.0\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"numba==0.65.1\" \\\n", + " \"numba==0.60.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynapple==0.7.1\" \\\n", " \"pynwb==2.8.3\" \\\n", @@ -113,30 +113,31 @@ " \"pyparsing==3.3.2\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", - " \"rich==15.0.0\" \\\n", + " \"rich==13.9.4\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"seaborn==0.13.2\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"tabulate==0.10.0\" \\\n", + " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n", diff --git a/tutorials/cosyne_2023/simple_dandiset_search.ipynb b/tutorials/cosyne_2023/simple_dandiset_search.ipynb index 48272df..9977a67 100644 --- a/tutorials/cosyne_2023/simple_dandiset_search.ipynb +++ b/tutorials/cosyne_2023/simple_dandiset_search.ipynb @@ -40,11 +40,11 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -52,28 +52,26 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,57 +87,56 @@ " \"jupyterlab-widgets==3.0.16\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\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", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", diff --git a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb index 49f3941..6a11eff 100644 --- a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb +++ b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb @@ -40,11 +40,11 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -52,28 +52,26 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", " \"hdmf-zarr==0.11.3\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,58 +87,58 @@ " \"jupyterlab-widgets==3.0.16\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.6.3\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==3.0.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\n", " \"pygments==2.20.0\" \\\n", " \"pynwb==2.8.3\" \\\n", " \"pyout==0.8.1\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", - " \"scipy==1.17.1\" \\\n", + " \"scipy==1.16.3\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", diff --git a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb index df8aeac..29f599b 100644 --- a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb +++ b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb @@ -40,11 +40,11 @@ " \"annotated-types==0.7.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", - " \"asttokens==3.0.1\" \\\n", " \"attrs==26.1.0\" \\\n", + " \"backcall==0.2.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -52,28 +52,26 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"comm==0.2.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", - " \"decorator==5.2.1\" \\\n", + " \"decorator==4.4.2\" \\\n", " \"deprecated==1.3.1\" \\\n", " \"dnspython==2.8.0\" \\\n", " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", - " \"executing==2.2.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", - " \"ipython==9.13.0\" \\\n", - " \"ipython-pygments-lexers==1.1.1\" \\\n", + " \"ipython==7.34.0\" \\\n", " \"ipywidgets==8.1.8\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,57 +87,56 @@ " \"jupyterlab-widgets==3.0.16\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"matplotlib-inline==0.2.2\" \\\n", + " \"matplotlib-inline==0.2.1\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", - " \"parso==0.8.7\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"parso==0.8.6\" \\\n", " \"pexpect==4.9.0\" \\\n", + " \"pickleshare==0.7.5\" \\\n", " \"platformdirs==4.9.6\" \\\n", " \"prompt-toolkit==3.0.52\" \\\n", - " \"propcache==0.5.2\" \\\n", - " \"psutil==7.2.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pure-eval==0.2.3\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\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", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.2\" \\\n", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", " \"ruamel-yaml==0.19.1\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", + " \"setuptools==75.2.0\" \\\n", " \"six==1.17.0\" \\\n", - " \"stack-data==0.6.3\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", - " \"traitlets==5.15.0\" \\\n", + " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"widgetsnbextension==4.0.15\" \\\n", " \"wrapt==2.1.2\" \\\n", diff --git a/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb b/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb index e03edf2..d00eadd 100644 --- a/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb +++ b/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb @@ -43,7 +43,7 @@ " \"attrs==26.1.0\" \\\n", " \"bids-validator-deno==2.4.1\" \\\n", " \"bidsschematools==1.2.2\" \\\n", - " \"blessed==1.39.0\" \\\n", + " \"blessed==1.38.0\" \\\n", " \"certifi==2026.4.22\" \\\n", " \"cffi==2.0.0\" \\\n", " \"charset-normalizer==3.4.7\" \\\n", @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==48.0.0\" \\\n", + " \"cryptography==43.0.3\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.75.1\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,12 +64,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2026.4.0\" \\\n", + " \"fsspec==2025.3.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.12.0\" \\\n", " \"humanize==4.15.0\" \\\n", - " \"idna==3.14\" \\\n", + " \"idna==3.13\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,35 +84,35 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.0\" \\\n", - " \"matplotlib==3.10.9\" \\\n", + " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.5.4\" \\\n", - " \"more-itertools==11.0.2\" \\\n", + " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.4.4\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", " \"opencv-python==4.13.0.92\" \\\n", - " \"packaging==26.2\" \\\n", - " \"pandas==2.3.3\" \\\n", - " \"pillow==12.2.0\" \\\n", + " \"packaging==26.1\" \\\n", + " \"pandas==2.2.2\" \\\n", + " \"pillow==11.3.0\" \\\n", " \"platformdirs==4.9.6\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.4.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", - " \"pydantic-settings==2.14.1\" \\\n", + " \"pydantic==2.12.3\" \\\n", + " \"pydantic-core==2.41.4\" \\\n", + " \"pydantic-settings==2.14.0\" \\\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", - " \"pytz==2026.2\" \\\n", + " \"pytz==2025.2\" \\\n", " \"pyyaml==6.0.3\" \\\n", " \"referencing==0.37.0\" \\\n", " \"remfile==0.1.13\" \\\n", - " \"requests==2.34.0\" \\\n", + " \"requests==2.32.4\" \\\n", " \"rfc3339-validator==0.1.4\" \\\n", " \"rfc3987==1.3.8\" \\\n", " \"rpds-py==0.30.0\" \\\n", @@ -121,15 +121,15 @@ " \"semantic-version==2.10.0\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", - " \"tensorstore==0.1.83\" \\\n", + " \"tensorstore==0.1.82\" \\\n", " \"threadpoolctl==3.6.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.15.0\" \\\n", " \"typing-inspection==0.4.2\" \\\n", - " \"tzdata==2026.2\" \\\n", + " \"tzdata==2026.1\" \\\n", " \"uri-template==1.3.0\" \\\n", - " \"urllib3==2.7.0\" \\\n", - " \"wcwidth==0.7.0\" \\\n", + " \"urllib3==2.5.0\" \\\n", + " \"wcwidth==0.6.0\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"wrapt==2.1.2\" \\\n", " \"yarl==1.23.0\" \\\n",