Standardizing autism research data into NWB and Spyglass
The Simons Foundation Autism Research Initiative (SFARI) funds CatalystNeuro to standardize data from labs in its Autism Rat Models Consortium (ARC). SFARI established the consortium in 2022 to study behavior and circuits relevant to autism in rat lines carrying CRISPR/Cas9 loss-of-function mutations in high-confidence autism risk genes. Since October 2024 we have been converting ARC data to Neurodata Without Borders (NWB) and making the files compatible with Spyglass, the DataJoint-based analysis framework developed in Loren Frank’s lab, working with the Flatiron Institute’s research software engineers to use them as source data in Spyglass pipelines.
The project now spans nine labs in the United States, Canada, and the United Kingdom, most of them working with rat models such as Fmr1 knockout rats. The data include SpikeGadgets, Open Ephys, and Neuropixels recordings, multi-day wireless EEG, fiber photometry, Miniscope imaging, and multi-camera video with DeepLabCut, MoSeq, and DANNCE pose estimation. We write each conversion to meet the requirements Spyglass places on NWB files and collect reusable interfaces in the neuroconv-spyglass repository. The first complete dataset, on the head-direction signal in juvenile and adult Fmr1 knockout rats, is published as Dandiset 001699. We also contribute fixes upstream to Spyglass, have opened a discussion with its developers on supporting EEG, and are developing an NWB extension for sleep staging.
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 Ölveczky
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.