Merge pull request #104 from catalystneuro/leifer

Add 001075 example figure
dandi · Oct 1, 2024 · 10c444a · 10c444a
2 parents c079629 + 89b2791
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diff --git a/001075/001075_notebook_environment.yml b/001075/001075_notebook_environment.yml
@@ -0,0 +1,187 @@
+name: leifer_notebooks_created_8_29_2024
+channels:
+  - defaults
+dependencies:
+  - bzip2=1.0.8=h2bbff1b_6
+  - ca-certificates=2024.7.2=haa95532_0
+  - expat=2.6.2=hd77b12b_0
+  - libffi=3.4.4=hd77b12b_1
+  - openssl=3.0.14=h827c3e9_0
+  - pip=24.2=py312haa95532_0
+  - python=3.12.4=h14ffc60_1
+  - setuptools=72.1.0=py312haa95532_0
+  - sqlite=3.45.3=h2bbff1b_0
+  - tk=8.6.14=h0416ee5_0
+  - vc=14.40=h2eaa2aa_0
+  - vs2015_runtime=14.40.33807=h98bb1dd_0
+  - wheel=0.43.0=py312haa95532_0
+  - xz=5.4.6=h8cc25b3_1
+  - zlib=1.2.13=h8cc25b3_1
+  - pip:
+      - aiobotocore==2.14.0
+      - aiohappyeyeballs==2.4.0
+      - aiohttp==3.10.5
+      - aioitertools==0.11.0
+      - aiosignal==1.3.1
+      - annotated-types==0.7.0
+      - anyio==4.4.0
+      - argon2-cffi==23.1.0
+      - argon2-cffi-bindings==21.2.0
+      - arrow==1.3.0
+      - asciitree==0.3.3
+      - asttokens==2.4.1
+      - async-lru==2.0.4
+      - attrs==24.2.0
+      - babel==2.16.0
+      - beautifulsoup4==4.12.3
+      - bidsschematools==0.7.2
+      - bleach==6.1.0
+      - botocore==1.35.7
+      - certifi==2024.8.30
+      - cffi==1.17.0
+      - charset-normalizer==3.3.2
+      - ci-info==0.3.0
+      - click==8.1.7
+      - click-didyoumean==0.3.1
+      - colorama==0.4.6
+      - comm==0.2.2
+      - contourpy==1.3.0
+      - cycler==0.12.1
+      - dandi==0.63.1
+      - dandischema==0.10.3
+      - debugpy==1.8.5
+      - decorator==5.1.1
+      - defusedxml==0.7.1
+      - dnspython==2.6.1
+      - email-validator==2.2.0
+      - etelemetry==0.3.1
+      - executing==2.0.1
+      - fasteners==0.19
+      - fastjsonschema==2.20.0
+      - fonttools==4.53.1
+      - fqdn==1.5.1
+      - frozenlist==1.4.1
+      - fscacher==0.4.1
+      - fsspec==2024.6.1
+      - h11==0.14.0
+      - h5py==3.11.0
+      - hdmf==3.14.3
+      - hdmf-zarr==0.8.0
+      - httpcore==1.0.5
+      - httpx==0.27.2
+      - humanize==4.10.0
+      - idna==3.8
+      - interleave==0.2.1
+      - ipykernel==6.29.5
+      - ipython==8.26.0
+      - ipywidgets==8.1.5
+      - isodate==0.6.1
+      - isoduration==20.11.0
+      - jaraco-classes==3.4.0
+      - jaraco-context==6.0.1
+      - jaraco-functools==4.0.2
+      - jedi==0.19.1
+      - jinja2==3.1.4
+      - jmespath==1.0.1
+      - joblib==1.4.2
+      - json5==0.9.25
+      - jsonpointer==3.0.0
+      - jsonschema==4.23.0
+      - jsonschema-specifications==2023.12.1
+      - jupyter==1.1.0
+      - jupyter-client==8.6.2
+      - jupyter-console==6.6.3
+      - jupyter-core==5.7.2
+      - jupyter-events==0.10.0
+      - jupyter-lsp==2.2.5
+      - jupyter-server==2.14.2
+      - jupyter-server-terminals==0.5.3
+      - jupyterlab==4.2.5
+      - jupyterlab-pygments==0.3.0
+      - jupyterlab-server==2.27.3
+      - jupyterlab-widgets==3.0.13
+      - keyring==25.3.0
+      - keyrings-alt==5.0.2
+      - kiwisolver==1.4.5
+      - markupsafe==2.1.5
+      - matplotlib==3.9.2
+      - matplotlib-inline==0.1.7
+      - mistune==3.0.2
+      - more-itertools==10.4.0
+      - multidict==6.0.5
+      - natsort==8.4.0
+      - nbclient==0.10.0
+      - nbconvert==7.16.4
+      - nbformat==5.10.4
+      - nest-asyncio==1.6.0
+      - notebook==7.2.2
+      - notebook-shim==0.2.4
+      - numcodecs==0.13.0
+      - numpy==1.26.4
+      - nwbinspector==0.5.1
+      - overrides==7.7.0
+      - packaging==24.1
+      - pandas==2.2.2
+      - pandocfilters==1.5.1
+      - parso==0.8.4
+      - pillow==10.4.0
+      - platformdirs==4.2.2
+      - prometheus-client==0.20.0
+      - prompt-toolkit==3.0.47
+      - psutil==6.0.0
+      - pure-eval==0.2.3
+      - pycparser==2.22
+      - pycryptodomex==3.20.0
+      - pydantic==2.8.2
+      - pydantic-core==2.20.1
+      - pygments==2.18.0
+      - pynwb==2.8.1
+      - pyout==0.7.3
+      - pyparsing==3.1.4
+      - python-dateutil==2.9.0.post0
+      - python-json-logger==2.0.7
+      - pytz==2024.1
+      - pywin32==306
+      - pywin32-ctypes==0.2.3
+      - pywinpty==2.0.13
+      - pyyaml==6.0.2
+      - pyzmq==26.2.0
+      - referencing==0.35.1
+      - remfile==0.1.13
+      - requests==2.32.3
+      - rfc3339-validator==0.1.4
+      - rfc3986-validator==0.1.1
+      - rfc3987==1.3.8
+      - rpds-py==0.20.0
+      - ruamel-yaml==0.18.6
+      - ruamel-yaml-clib==0.2.8
+      - s3fs==2024.6.1
+      - scipy==1.14.1
+      - semantic-version==2.10.0
+      - send2trash==1.8.3
+      - six==1.16.0
+      - sniffio==1.3.1
+      - soupsieve==2.6
+      - stack-data==0.6.3
+      - tenacity==9.0.0
+      - terminado==0.18.1
+      - threadpoolctl==3.5.0
+      - tinycss2==1.3.0
+      - tornado==6.4.1
+      - tqdm==4.66.5
+      - traitlets==5.14.3
+      - types-python-dateutil==2.9.0.20240821
+      - typing-extensions==4.12.2
+      - tzdata==2024.1
+      - uri-template==1.3.0
+      - urllib3==2.2.2
+      - wcwidth==0.2.13
+      - webcolors==24.8.0
+      - webencodings==0.5.1
+      - websocket-client==1.8.0
+      - widgetsnbextension==4.0.13
+      - wrapt==1.16.0
+      - yarl==1.9.4
+      - zarr==2.18.2
+      - zarr-checksum==0.4.2
+prefix: C:\Users\theac\anaconda3\envs\leifer_notebooks_created_8_29_2024
diff --git a/001075/001075_paper_figure_1d.ipynb b/001075/001075_paper_figure_1d.ipynb
diff --git a/001075/README.md b/001075/README.md
@@ -0,0 +1,54 @@
+# 001075 - Neural signal propagation atlas of Caenorhabditis elegans
+
+## How to cite
+
+Randi, Francesco; Sharma, Anuj; Dvali, Sophie; Leifer, Andrew M. (2024) Neural signal propagation atlas of Caenorhabditis elegans (Version 0.240930.1859) [Data set]. DANDI archive. https://doi.org/10.48324/dandi.001075/0.240930.1859
+
+
+
+## Setup
+
+Install [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) on your machine. 
+Install `git` and clone the example notebook repository:
+
+```bash
+conda install git
+git clone https://github.com/dandi/example-notebooks.git
+```
+
+Then create a specific environment for this notebook using:
+
+```bash
+conda env create --file example-notebooks/001075/001075_notebook_environment.yml
+```
+
+Then activate the environment:
+
+```bash
+conda activate leifer_notebooks_created_8_29_2024
+```
+
+Finally, start Jupyter:
+
+```bash
+jupyter notebook
+```
+
+And select the notebook `001075_paper_figure_1d.ipynb` from the file explorer in the browser.
+
+If interested in creating your own plots, refer to the code in `utils_001075` for how to handle the data streams.
+
+Note that all timing information is aligned to the NeuroPAL imaging system.
+
+
+
+## Help
+
+- Dataset: https://dandiarchive.org/dandiset/001075/0.240930.1859
+- Original publication: [Neural signal propagation atlas of Caenorhabditis elegans](https://www.nature.com/articles/s41586-023-06683-4)
+- [Visualize (Neurosift)](https://neurosift.app/?p=/dandiset&dandisetId=001075&dandisetVersion=0.240930.1859)
+  - Note: the files are split by 'imaging' (raw) and 'segmentation' (processed). To view both, select a combined 
+    view for the same session: [example](https://neurosift.app/?p=/nwb&url=https://api.dandiarchive.org/api/assets/5feda038-0c84-494a-a0e0-c3ef8ec194d1/download/&url=https://api.dandiarchive.org/api/assets/40a6799b-4835-4170-89bb-9a866082e503/download/&dandisetId=001075&dandisetVersion=draft). 
+- [NWB file basics](https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_file.html#sphx-glr-tutorials-general-plot-file-py)
+- [How to read NWB files](https://pynwb.readthedocs.io/en/stable/tutorials/general/scratch.html#sphx-glr-tutorials-general-scratch-py)
+- [Data analysis with NWB files](https://pynwb.readthedocs.io/en/stable/tutorials/general/scratch.html#sphx-glr-tutorials-general-scratch-py)
diff --git a/001075/utils_001075/__init__.py b/001075/utils_001075/__init__.py
@@ -0,0 +1,4 @@
+from ._waterfall import plot_waterfall
+from ._stream_nwbfile import stream_nwbfile
+
+__all__ = ["plot_waterfall", "stream_nwbfile"]
diff --git a/001075/utils_001075/_stream_nwbfile.py b/001075/utils_001075/_stream_nwbfile.py
@@ -0,0 +1,21 @@
+from typing import Literal
+
+import dandi.dandiapi
+import h5py
+import pynwb
+import remfile
+
+def stream_nwbfile(subject_id: str, session_id: str, session_type: Literal["imaging", "segmentation"]) -> pynwb.NWBFile:
+    dandiset_id = "001075"
+    dandifile_path = f"sub-{subject_id}/sub-{subject_id}_ses-{session_id}_desc-{session_type}_ophys+ogen.nwb"
+
+    dandi_client = dandi.dandiapi.DandiAPIClient()
+    dandiset = dandi_client.get_dandiset(dandiset_id=dandiset_id)
+    dandifile = dandiset.get_asset_by_path(path=dandifile_path)
+    s3_url = dandifile.get_content_url()
+    byte_stream = remfile.File(url=s3_url)
+    file = h5py.File(name=byte_stream)
+    io = pynwb.NWBHDF5IO(file=file)
+    nwbfile = io.read()
+
+    return nwbfile