All NWB conversions

Alexandra Nelson

University of California, San Francisco

Project started October 2023

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.

Data and methods
Mousebehavioral trackingelectrophysiologyParkinson's disease
Conversion code
nelson-lab-to-nwb
Published datasets
Funded under
Aligning Science Across Parkinson's
Scope of work

The Nelson lab has collected electrophysiological data using optogenetically labeled single-unit recordings in freely moving mice in an open field, as part of the ASAP initiative. Our goals are to package this data at each stage of processing in the NWB format so that it can be shared within the lab and published on the DANDI Archive.

Conversion of Electrophysiology and Behavior

We wrote an open-source Python package to ingest the data the lab is collecting with the systems used in their paper “Aberrant Striatal Activity in Parkinsonism and Levodopa-Induced Dyskinesia”. The conversion covers single-unit activity from microwires on a 32-channel Plexon MAP system; Plexon spike sorting output; video recordings and gross behavior tracking from Noldus EthoVision; fine behavior manually scored by the experimenter as AIM scores; Arduino-controlled TTL optical stimuli; TDT fiber photometry; and the TTL synchronization pulses triggered by the video tracking software and recorded by the electrophysiology system.

Additional Interfaces

We also created interfaces, or tested existing ones against the lab’s data, for a wider set of formats the lab works with: Igor Pro ex-vivo recordings, Intan, Blackrock, Doric photometry and Miniscope files, and histology images from Nikon, Olympus, and Zeiss microscopes.

Publication on DANDI

We created a pipeline that uploads the converted sessions relating to the paper to the DANDI Archive. On completion the dataset is published on the lab’s behalf, with a minted DOI.

Demonstrating NWB Usage

We created Jupyter notebooks demonstrating how to read the converted files and access each data stream.

Related work

Daniel Dombeck

Northwestern University

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.

Helen N. Schwerdt

University of Pittsburgh

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.

Jacob Reimer

Baylor College of Medicine

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.

Jim Surmeier

Northwestern University

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.