Standardizing autism research data into NWB and Spyglass
A collaborative project funded by the Simons Foundation Autism Research Initiative (SFARI) to integrate neuroscience data into standardized NWB format and Spyglass database systems. The project focuses on converting complex behavioral and electrophysiology datasets from multiple experiments, enabling better data sharing and analysis across the neuroscience community. This work includes developing robust conversion pipelines that ensure compatibility with both NWB standards and Spyglass analysis frameworks.
NWB conversions under this project
9 labs
Naoshige Uchida
Harvard University
Developing NWB conversion tools for the Uchida lab's behavioral and fiber photometry datasets studying social behavior and observational fear learning. The conversion pipeline handles fiber photometry from Doric hardware (raw and processed MATLAB signals), multi-camera behavioral video (six cameras), DANNCE / social-DANNCE pose estimation, pCampi synchronization data (H5 files with TTL pulses), stimulus and trial event data (e.g., foot shock times), and subject metadata, with Neuropixels electrophysiology (SpikeGLX) including spike-sorted output and trial structure as a stretch goal. The pipeline performs time alignment across data streams and adapts conversions for ingestion into a Spyglass analysis pipeline.
Bence Olveczky
Harvard University
Developing NWB conversion tools for the Olveczky lab's behavioral and electrophysiological datasets studying learned and natural behaviors. The pipeline standardizes 256-channel flexible probe and Neuropixels recordings, continuous tetrode data, six-camera video with sDANNCE pose estimation, and trial structure, and adapts the resulting files for ingestion into a Spyglass pipeline.
Paul Dudchenko
University of Stirling
Developed NWB conversion pipelines and analysis workflows for the Dudchenko lab's rodent navigation experiments studying age-dependent alterations in the head-direction signal in Fmr1-/y rats, a model of Fragile X Syndrome, as part of a Simons Foundation SFARI ARC project. The conversion standardized OpenEphys extracellular electrophysiology, spiking units, Bonsai behavioral tracking, sleep-state classification from processed LFP, video, and histology from juvenile and adult rats. The pipeline conformed the data to NWB best practices and made it fully Spyglass compatible, leveraged NeuroConv's backend configuration for state-of-the-art chunking and compression, and published the full dataset to the DANDI Archive along with example notebooks and documentation for the Autism Rat Models Consortium and broader neuroscience community.
Tim Hanks
University of California, Davis
Developing NWB conversion tools for the Hanks lab's behavioral and fiber photometry datasets studying decision-making and working memory in rats. The pipeline standardizes multi-region Doric photometry recordings, Bpod trial data read from the lab's SQL database, behavioral video, and pose estimation outputs, and adapts the resulting files for ingestion into a Spyglass pipeline.
Adrien Peyrache
McGill University
Converting the Peyrache lab's raw Miniscope calcium imaging data to NWB and linking it to the processed outputs already published on DANDI, alongside development of an NWB extension for sleep data. The extension formalizes sleep stage annotations, staging method metadata, and sub-stage descriptors, with the lab's sleep recordings converted as a reference implementation.
Alfredo Gonzalez-Sulser
University of Edinburgh
Developing NWB conversion tools for the Gonzalez-Sulser lab's chronic EEG recordings across multiple SFARI rat lines, studying circadian rhythms, sleep-wake cycles, and seizure activity. The pipeline standardizes multi-day wireless TainiTec recordings alongside the lab's automated sleep state classifications and seizure timestamps, and adapts the resulting files for ingestion into a Spyglass pipeline.
Peter Kind
University of Edinburgh
Converting multimodal neuroscience data including extracellular electrophysiology recordings from OpenEphys/Intan systems, behavioral scoring data, video recordings with MoSeq pose estimation, and sensory stimulation data. The conversion pipeline ensures compatibility with Spyglass for advanced analysis capabilities.
Marino Pagan
University of Edinburgh
Developing NWB conversion tools for the Pagan lab's research on flexible decision-making in SFARI Autism Rat Models. The pipeline standardizes behavioral data from the Bcontrol system, behavioral video recordings, and future electrophysiological data from SpikeGadgets. These tools facilitate data sharing within the lab and publication on the DANDI Archive, while ensuring compatibility with Spyglass pipelines for reliable analysis.
Shantanu Jadhav
Brandeis University
Converted behavior and electrophysiology data from multiple projects, including integration with Spyglass as part of a Simons Foundation SFARI ARC project. The first dataset includes behavioral tracking, video recordings, spike sorting, and LFP recordings from experiments studying neural mechanisms of learning and memory. The second dataset focuses on pro-social behaviors in wild-type and Fmr1-/y rat pairs performing cooperative tasks on W mazes to obtain joint rewards, aiming to investigate the neural mechanisms underlying social interaction deficits associated with autism spectrum disorders.