Add Zhai 2025 analysis notebooks for DANDI:001538 - #121
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h-mayorquin
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Sep 2, 2025
h-mayorquin
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- figure_1E_dspn_somatic_excitability.ipynb: Reproduces Figure 1E somatic excitability analysis
- figure_2GH_oepsc_analysis.ipynb: Reproduces Figure 2G-H oEPSC analysis
- figure_5F_acetylcholine_biosensor.ipynb: Reproduces Figure 5F acetylcholine biosensor analysis
- how_to_use_this_dataset.ipynb: Introduction and data exploration tutorial
- environment.yml: Conda environment with all dependencies
- README.md: Documentation explaining the notebooks and publication
- figure_1E_dspn_somatic_excitability.ipynb: Reproduces Figure 1E somatic excitability analysis - figure_2GH_oepsc_analysis.ipynb: Reproduces Figure 2G-H oEPSC analysis - figure_5F_acetylcholine_biosensor.ipynb: Reproduces Figure 5F acetylcholine biosensor analysis - how_to_use_this_dataset.ipynb: Introduction and data exploration tutorial - environment.yml: Conda environment with all dependencies - README.md: Documentation explaining the notebooks and publication
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@h-mayorquin it looks like the corresponding paper has been published: https://www.biorxiv.org/content/10.1101/2025.01.02.631090v2 https://www.science.org/doi/10.1126/sciadv.adv8224 Could you please follow up with the lab to see if they want us to unembargo the dataset and merge this PR? |
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Amazing, I will contact them. |
bendichter
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May 27, 2026 13:03
CI walks every notebook and requires a pinned `!uv pip install --system` bootstrap cell (PR dandi#149 pattern); these four were missing it and failed at the extract stage. Add the standard 4-cell bootstrap (Colab badge, install intro, pinned install cell, restart admonition) to each notebook. Pins resolved on Python 3.12 with numpy==2.0.2 to match the Colab runtime; matplotlib and pandas held to the <3.11 / <3 lines the notebooks were written against (matplotlib 3.11 removed the boxplot `labels=` kwarg figure_1E uses). Also wrap remfile.File with a DiskCache("nwb-cache") so repeated streams within a run are served from disk, and normalize all notebooks to nbformat_minor 5 (figure_5F was minor 4 with id-bearing cells). All four verified end-to-end via .github/scripts/run_notebook.py (ok: true). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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