Example Notebooks for 001699 (embargoed)

001699/README.md

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+# Example Sessions for Dandiset 001699
+
+This submission provides four notebooks showcasing example sessions for the Dandiset 001699. The notebooks cover both age groups (juvenile and adult) and both genotypes (wild-type and Fmr1 knockout).
+
+The notebooks provide examples of how to access the critical data and metadata from the sessions in the dataset:
+
+- `example_notebook_juvenile_wt.ipynb` showcases an example juvenile wild-type session (subject H3022, session H3022-210806) containing task epochs, position tracking, sleep classification, raw electrophysiology, LFP, spike-sorted units, and histology images.
+- `example_notebook_juvenile_ko.ipynb` showcases an example juvenile Fmr1 knockout session (subject H3016, session H3016-210422) containing task epochs, position tracking, sleep classification, raw electrophysiology, LFP, spike-sorted units, and histology images.
+- `example_notebook_adult_wt.ipynb` showcases an example adult wild-type session (subject H4813, session H4813-220728) containing task epochs, position tracking, sleep classification, raw electrophysiology, LFP, spike-sorted units, and histology images.
+- `example_notebook_adult_ko.ipynb` showcases an example adult Fmr1 knockout session (subject H4817, session H4817-220828) containing task epochs, position tracking, sleep classification, raw electrophysiology, LFP, spike-sorted units, and histology images.

001699/environment.yml

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+# run: conda env create --file environment.yml
+name: dudchenko_notebook_env
+channels:
+    - conda-forge
+dependencies:
+    - python==3.13
+    - ipykernel
+    - matplotlib
+    - numpy
+    - pip
+    - pip:
+      - dandi
+      - remfile
+      - pynwb

001699/stream_nwbfile.py

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+from pynwb import NWBHDF5IO
+import remfile
+import h5py
+from dandi.dandiapi import DandiAPIClient
+
+def stream_nwbfile(DANDISET_ID, file_path):
+    '''Stream NWB file from DANDI archive.
+
+    Parameters
+    ----------
+    DANDISET_ID : str
+        Dandiset ID
+    file_path : str
+        Path to NWB file in DANDI archive
+
+    Returns
+    -------
+    nwbfile : NWBFile
+        NWB file
+    io : NWBHDF5IO
+        NWB IO object (for closing)
+
+    Notes
+    -----
+    The io object must be closed after use.
+    '''
+    with DandiAPIClient() as client:
+        client.dandi_authenticate()
+        asset = client.get_dandiset(DANDISET_ID, 'draft').get_asset_by_path(file_path)
+        s3_url = asset.get_content_url(follow_redirects=1, strip_query=False)
+    file_system = remfile.File(s3_url)
+    file = h5py.File(file_system, mode="r")
+    io = NWBHDF5IO(file=file, load_namespaces=True)
+    nwbfile = io.read()
+    return nwbfile, io