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Add Turner Lab M1 motor cortex notebooks for dandiset 001636#147

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bendichter merged 3 commits intodandi:masterfrom
h-mayorquin:add_turner
May 5, 2026
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Add Turner Lab M1 motor cortex notebooks for dandiset 001636#147
bendichter merged 3 commits intodandi:masterfrom
h-mayorquin:add_turner

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@h-mayorquin
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This PR adds four notebooks under 001636/TurnerLab/motor_cortex/ for the Turner lab MPTP parkinsonism dataset (DANDI:001636), covering general usage, peri-event time histograms with pynapple, Poisson GLM encoding with NeMoS, and a background tutorial on antidromic cell-type identification. The README in the folder describes each notebook in more detail.

The accompanying environment.yml pins all dependencies (Python 3.12, numpy 2.2.6, pynwb 3.1.3, pynapple 0.10.3, nemos 0.2.6, jax 0.9.0.1, and the rest), and I have verified end-to-end that all four notebooks execute cleanly in a fresh conda env created from this file. One non-obvious pin is optimistix==0.0.11: optimistix 0.1.0 changed an internal API that breaks NeMoS 0.2.6's FISTA solver, so the older release is required for the GLM notebook to fit.

I have left the helper modules (notebook_helpers.py, trial_structure_plot.py) alongside the notebooks since they are imported directly by them.

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@h-mayorquin
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Codespell is unrelated to this.

@bendichter bendichter merged commit fd2e364 into dandi:master May 5, 2026
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@h-mayorquin h-mayorquin deleted the add_turner branch May 5, 2026 12:45
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2 participants