Parkinson's Disease (PD) Open Data Guide: Alpha-Synuclein Assays, Basal Ganglia LFP & Cohort Harmonization
Navigating MJFF pipelines, DANDI Archive electrophysiology (NWB), and OpenNeuro motor circuit neuroimaging.
Parkinson's disease (PD) spans a multi-decade continuum beginning with prodromal autonomic and REM sleep behavior disorder (RBD) phases long before classical nigrostriatal dopaminergic motor symptoms emerge. This guide details how to leverage open datasets across the Michael J. Fox Foundation (MJFF) ecosystem, DANDI Archive cellular/circuit electrophysiology, and OpenNeuro fMRI/EEG recordings.
1. Biochemical Staging: α-Synuclein SAA, LRRK2, and GBA1 Subtypes
- Distinguish ON-medication vs. OFF-medication states when analyzing MDS-UPDRS Part III motor scores or fMRI/EEG connectivity.
- Account for Levodopa Equivalent Daily Dose (LEDD) as a mandatory covariate in longitudinal progression models.
- Leverage DANDI NWB datasets to study pathological beta-band (13–30 Hz) oscillations in the subthalamic nucleus (STN).
2. Circuit Electrophysiology: Beta Bursts & Adaptive DBS on DANDI & OpenNeuro
3. Single-Cell Atlases of Substantia Nigra Vulnerability
Python Example: Beta-Band (13-30 Hz) Spectral Power & Burst Extraction with MNE / SciPy
Standard Python template ready for integration into local Jupyter notebooks or automated pipelines.
import numpy as np
from scipy.signal import butter, filtfilt, hilbert
def extract_beta_bursts(lfp_signal: np.ndarray, sfreq: float = 1000.0, threshold_percentile: float = 75.0):
"""Extract pathological beta-band (13-30 Hz) envelope and burst durations in Parkinsonian LFP."""
nyq = 0.5 * sfreq
b, a = butter(N=4, Wn=[13.0 / nyq, 30.0 / nyq], btype="band")
beta_filtered = filtfilt(b, a, lfp_signal)
# Compute analytic amplitude envelope via Hilbert transform
envelope = np.abs(hilbert(beta_filtered))
threshold = np.percentile(envelope, threshold_percentile)
is_burst = envelope > threshold
burst_fraction = np.mean(is_burst)
print(f"75th Percentile Threshold: {threshold:.2f} uV | Above-threshold fraction: {burst_fraction:.2%}")
return envelope, is_burstResearch Governance & Reproducibility Checklist
- Always document whether clinical/imaging assessments were performed in the dopaminergic ON or OFF state (>12h withdrawal).
- Include Levodopa Equivalent Daily Dose (LEDD) and disease duration since symptom onset as covariates.
- Separate genetic carriers (LRRK2, GBA1, SNCA, PRKN) from sporadic PD when training biomarker classifiers.
Key Biomarkers & Standards Referenced in This Guide
Presynaptic neuronal protein encoded by SNCA whose misfolding and fibrillar aggregation form Lewy bodies in Parkinson's disease and Lewy body dementia.
Multidomain kinase/GTPase protein; activating mutations (such as G2019S) are the most common cause of autosomal-dominant Parkinson's disease.
Comprehensive four-part clinical rating scale quantifying non-motor experiences, activities of daily living, motor examination (Part III), and motor complications in Parkinson's disease.
High-temporal-resolution recording of postsynaptic cortical electrical potentials and neural oscillations (delta, theta, alpha, beta, gamma bands).
Unified data standard for cellular neurophysiology, packaging intracellular/extracellular recordings, optical physiology, and behavior into HDF5/Zarr files.
High-throughput transcriptomic profiling at individual cell or nucleus resolution, enabling identification of disease-associated microglia (DAM), astrocytes, and vulnerable neuronal subtypes.
Live Open Datasets & Papers Matching This Guide
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OpenNeuro ds008896: Preprocessed EEG data in CLN3 disease and NIH healthy volunteers
BIDS neuroimaging dataset containing EEG scans from 95 Subjects. Freely available for computational neuroscience.
Not All Entropy Is Equal: Why Representation Matters for Biological Interpretation in Dementia EEG
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OpenNeuro ds008851: EEG Data for Emotion Recognition: Alcohol Cue-Reactivity Dataset (Alcohol Dependence vs Healthy Controls)
BIDS neuroimaging dataset containing EEG scans from 60 Subjects. Freely available for computational neuroscience.
OpenNeuro ds008940: Dietary identity and the neural categorization of food images: an open EEG dataset with Food-pics stimuli
BIDS neuroimaging dataset containing EEG scans from 77 Subjects. Freely available for computational neuroscience.