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23 changes: 23 additions & 0 deletions 001538/catalyst_neuro/zhai_2025/README.md
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# Analysis Notebooks for Zhai et al. 2025

## Goal

This submission provides Jupyter notebooks for reproducing key figures from **Zhai et al. 2025** using data from **DANDI:001538 - State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia**. The notebooks demonstrate how to analyze electrophysiology, optogenetics, and acetylcholine biosensor data to understand cellular mechanisms underlying levodopa-induced dyskinesia in Parkinson's disease.

## Publication

**Zhai et al. 2025** - *State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia*

## Notebooks

### `how_to_use_this_dataset.ipynb`
Introduction and data exploration tutorial showing how to access and browse the NWB files in DANDI:001538, extract metadata, and perform basic data visualization.

### `figure_1E_dspn_somatic_excitability.ipynb`
Reproduces Figure 1E analyzing somatic excitability in direct pathway striatal projection neurons (dSPNs). Generates frequency-intensity curves and rheobase measurements from current clamp recordings to show L-DOPA treatment effects on neuronal excitability.

### `figure_2GH_oepsc_analysis.ipynb`
Reproduces Figure 2G-H analyzing optogenetically-evoked postsynaptic currents (oEPSCs). Compares amplitude distributions and mean responses between off-state and on-state conditions using ChR2 optogenetic stimulation and voltage-clamp recordings.

### `figure_5F_acetylcholine_biosensor.ipynb`
Reproduces Figure 5F analyzing acetylcholine release dynamics using the GRABACh3.0 biosensor. Shows acetylcholine signaling alterations across control, Parkinsonian, and dyskinetic conditions with pharmacological modulation (dopamine, quinpirole, sulpiride).
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name: zhai2025_analysis
channels:
- conda-forge
- defaults
dependencies:
# Python (matching pyproject.toml requirements)
- python=3.12

# Core scientific computing
- numpy>=1.21.0
- pandas>=2.2.3
- scipy>=1.7.0

# Data visualization
- matplotlib>=3.10.3
- seaborn>=0.13.2

# HDF5 and file handling
- h5py>=3.1.0
- lxml
- tifffile>=2025.5.10
- openpyxl>=3.1.5

# Progress bars
- tqdm>=4.67.1

# Environment variables
- python-dotenv>=1.1.1

# Jupyter notebook support
- jupyter>=1.0.0
- ipykernel>=6.29.5
- ipywidgets>=7.6.0

# Image processing
- opencv-python-headless>=4.12.0.88
- imagecodecs>=2025.3.30

# Install via pip
- pip
- pip:
# DANDI API client
- dandi>=0.69.3

# NWB file format support
- pynwb>=2.1.0
- hdmf==4.0.0
- neuroconv>=0.7.4
- nwbinspector

# NWB streaming and remote access
- remfile>=0.1.13
- fsspec>=2021.10.0
- aiohttp>=3.8.0
- s3fs>=2021.10.0

# Additional dependencies from pyproject.toml
- nd2>=0.10.3
- xmltodict>=0.14.2
- roiextractors>=0.5.13
- astropy>=6.1.7
- ndx-optogenetics
- xarray>=2025.7.1
- tabulate>=0.9.0

# Additional analysis tools
- scikit-learn>=1.0.0
- statsmodels>=0.13.0
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