Aligning Science Across Parkinson's

Comprehensive NWB conversion tools for the Turner lab's electrophysiology datasets from parkinsonian macaque studies. The conversion pipeline handles three distinct experimental paradigms: (1) Multi-area recordings (motor cortex, striatum, STN, GPi/GPe) during center-out reaching tasks with TDT recording systems, (2) Motor cortex single-unit recordings with antidromic cell-type identification (pyramidal tract and corticostriatal neurons) during visuomotor step-tracking with muscle stretch perturbations, and (3) Further datasets with specialized behavioral protocols. Includes custom NWB extension (ndx-turner-metadata) for lab-specific metadata, specialized interfaces for TDT recordings with filtered/raw data streams, and MATLAB-based electrophysiology data with trial-aligned analog signals (kinematics, EMG, LFP). Tools support multi-session experiments with interactive tutorials for data visualization and analysis.

Developed NWB conversion tools for Schwerdt Lab's multi-modal neurochemical and electrophysiology datasets from rhesus monkeys. The pipeline supports conversion of fast-scan cyclic voltammetry (FSCV) signals, extracellular electrophysiology (Neuralynx) recordings from chronic striatal implants, spike times, and behavioral task events during reward-biased eye movement tasks.

Developed NWB conversion tools for the Meletis lab's multi-modal datasets studying dopaminergic circuits. The conversion pipeline handles fiber photometry data recording calcium transients from DAT+ and Anxa1+ terminals in the striatum, as well as dopamine release using dLight1.3. The tools also process behavioral data from multiple tasks including Water Consumption, Open Field Tests with DeepLabCut pose estimation and VAME behavioral classification, Arrow Maze Choice Tasks, and Forelimb Reaching Tasks.

NWB conversion pipeline for Surmeier lab's multimodal ex-vivo brain slice recordings from a mouse model of Parkinson's disease and levodopa-induced dyskinesia. The dataset includes patch-clamp electrophysiology (somatic and dendritic excitability), two-photon calcium imaging (standard imaging and line scans) with simultaneous electrophysiology, acetylcholine biosensor recordings (GRABACh3.0), confocal microscopy for spine density analysis, optogenetic stimulation, behavioral scoring (AIM scores and contralateral rotations), and video recordings. Data encompasses direct and indirect pathway spiny projection neurons (dSPNs and iSPNs) from the dorsolateral striatum in 6-OHDA lesioned mice with chronic levodopa treatment. All protocols are linked to protocols.io documentation.

Developing NWB conversion tools for the Khaliq lab's ex-vivo primate research. The pipeline standardizes patch clamp electrophysiology recordings in ABF format, calcium imaging data from Bruker systems (TIFF files), synchronization TTL pulses, and pharmacological data. These tools enable comprehensive analysis of hundreds of individual cells and facilitate data sharing through the DANDI Archive, with future plans for interactive Neurosift visualizations.

Developed NWB conversion tools for the Dan lab's sleep-wake project. The pipeline standardizes multiple data streams including EEG, EMG, fiber photometry, optogenetic stimulation data, behavioral videos, and DeepLabCut pose estimation. These tools enable comprehensive analysis of brain activity during sleep and wakefulness, facilitating data sharing through the DANDI Archive with example visualization notebooks for exploring the data relationships across modalities. This project culminated in two Dandisets: The first (#001617) focuses on the neural dynamics of sleep-wake regulation, as recorded by EEG, EMG, and fiber photometry, and probed by optogenetic stimulation. The second (#001711) centers on behavioral outcomes as captured by video and pose estimation data, alongside EEG and EMG recordings.

Developing NWB conversion tools for the Hnasko lab's research on fiber photometry alongside behavioral measurements. The pipeline standardizes data from TDT systems (fiber photometry and TTL pulses), behavioral videos from AnyMaze, synchronization signals, histology images from Zeiss microscopes, and in-progress work on processed fiber photometry data and pose estimation. These tools enable comprehensive analysis of neural activity in relation to behavior and facilitate data sharing through the DANDI Archive.

Developed NWB conversion tools for the Bevan lab's subthalamic nucleus recordings during freely moving locomotion. The pipeline standardizes Neuralynx electrophysiology with optogenetic stimulation, Plexon spike sorting, treadmill signals, high frame rate behavioral video, DeepLabCut pose estimation, and CCF registration, and handles recording segments in which the electrodes sit at different positions.

Developed NWB conversion tools for the Howe lab's neurophysiology datasets studying neural circuits involved in learning and decision-making. The conversion pipeline handles multi-modal data including neural recordings and behavioral measurements during complex behavioral tasks.

Developed NWB conversion tools for the Reimer lab's two-photon imaging datasets. The conversion pipeline handles complex datasets including calcium imaging from the two-photon random access mesoscope (2P-RAM), behavioral measurements (locomotion, eye tracking), and olfactory stimuli. The tools support the standardization of large-scale imaging experiments involving tens of thousands of neurons across multiple visual cortical areas.

Developed NWB conversion tools for the Dombeck lab's fiber photometry datasets studying dopamine neuron subtypes. The conversion pipeline handles multi-modal data including GCaMP6f calcium signals, behavioral measurements, and genetic subtype information from the substantia nigra and striatum during reward and movement tasks.

Developed NWB conversion tools for the Lerner lab's neuroscience datasets studying dopamine circuits and compulsive behavior. The conversion pipeline handles multi-modal data including fiber photometry recordings from striatal regions, optogenetic manipulations, and behavioral measurements during reward learning tasks.

Developed NWB conversion tools for the Nelson lab's behavioral neuroscience datasets. The conversion pipeline integrates multiple data streams including TDT electrophysiology recordings, Noldus behavioral tracking data, AIM scoring, and behavioral video recordings. The tools support both interactive notebook-based workflows and scriptable conversion processes, enabling efficient standardization of complex behavioral experiments.

Developed NWB conversion tools for the Higley lab's neurophysiology datasets, including the Lohani 2022 study which combines behavioral measurements with neural recordings. The conversion pipeline handles multi-modal data integration and implements custom behavioral interfaces for specialized experimental protocols.