NWB conversions

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Developed NWB conversion tools for the Suver lab's research on flight control and sensory integration in Drosophila. The pipeline standardizes whole-cell patch clamp recordings with seal tests, multi-camera video with DeepLabCut tracking, and tachometer, puffer, and photodiode signals from airflow and optic flow behavioral experiments.

Developed NWB conversion tools for the Kim lab's research on Drosophila visual processing. The pipeline standardizes two-photon imaging data, behavioral videos, and visual stimulus information. These tools integrate synchronization signals from MATLAB files and fluorescence traces from segmented regions of interest, facilitating analysis of neural responses to visual stimuli in relation to behavioral outputs.

Developed NWB conversion tools for the Dickerson lab's research on Drosophila sensory processing. The pipeline standardizes two-photon imaging of GCaMP7f and tdTomato from a Thorlabs microscope run by ThorImageLS, together with wingbeat amplitude and visual stimulus signals recorded by ThorSync.

Developed NWB conversion tools for multi-modal neuroscience data including behavioral tracking, electrophysiology recordings, optogenetic stimulation, intrinsic signal imaging, and auditory stimulation. The project includes conversion of behavioral data from .mat files, OpenEphys recordings, optogenetic stimulation parameters, intrinsic signal images, and auditory stimulation data from multiple experimental paradigms. These tools support experiments investigating how the auditory cortex integrates sound and movement information, encodes error and learning signals, and guides sensorimotor adaptation during skilled, sound-generating behaviors in mice.

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.

Converting multimodal neuroscience data including calcium imaging with Miniscope, EMG/EEG recordings, and behavioral tracking. The dataset includes sleep phase analysis, freezing behavior tracked with EZTrack, motion series data, and preprocessed imaging data using Minian for segmentation and calcium event detection.

Developed NWB conversion tools for the Cohen lab's free-flight optogenetics experiments in Drosophila. The pipeline standardizes wing and body angles reconstructed from high-speed video, LED stimulation, and driver and effector line metadata, along with Zeiss confocal images used to confirm the optogenetic lines.

Developed NWB conversion tools for the Fox lab's research on flight control and sensory integration in Drosophila. The pipeline standardizes high-speed video from three cameras, DeepLabCut tracking of the antennae and a haltere, and wingbeat amplitude, frequency, and photodiode signals, aligned using camera triggers recorded in the acquisition file.

Developed comprehensive NWB conversion tools for the Constantinople lab's diverse neuroscience datasets. The conversion pipeline handles multiple data streams including fiber photometry recordings and electrophysiology data, with support for both processed behavioral data and spike sorting. The tools include specialized extractors and interfaces for different experimental paradigms, along with extensive metadata handling through YAML configuration files.

Developed NWB conversion tools for the DiCarlo lab's neuroscience datasets. The conversion pipeline processes data from Macaca mulatta (rhesus macaques), including Utah array recordings acquired using the Intan data acquisition system, behavioral data encoded in the MWorks format, and visual stimuli presented as images or video. Additionally, the pipeline incorporates an optimized spike-threshold crossing algorithm and tools for calculating peristimulus time histograms (PSTH).

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 Leifer lab's C. elegans neural imaging datasets. The conversion pipeline handles complex whole-brain calcium imaging data combined with optogenetic stimulation, supporting systematic mapping of neural signal propagation across thousands of neuron pairs in the worm nervous system.

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.

Building NWB conversion pipelines for the Geffen lab's studies of auditory processing, covering electrophysiology, optogenetics, and multi-modal stimuli. Some streams arrive in common formats such as Intan, while task structure is held in the lab's own MATLAB structs, so the pipeline combines NeuroConv interfaces with custom ones.

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 Adesnik lab's MouseV1 project, which combines two-photon calcium imaging with two-photon holographic optogenetics in mouse primary visual cortex. The conversion covers ScanImage imaging, Suite2p segmentation, visual stimuli, and holographic stimulation stored with the ndx-patterned-ogen extension, across retinotopic mapping, orientation tuning, and ensemble stimulation epochs.

Developed NWB conversion tools for large-scale two-photon calcium imaging datasets from the Allen Brain Observatory. The project includes conversion of multi-layer recordings from different cell types in mouse visual cortex, handling complex data including cellular responses, running behavior, and visual stimulation parameters across multiple brain areas.

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.

Developed NWB conversion tools for the Clandinin lab's whole-brain imaging data in Drosophila, featuring volumetric two-photon calcium imaging while flies walked on an air-suspended ball. The conversion includes custom interfaces for the lab's NIfTI imaging files and Bruker metadata, processed brain volumes registered to an atlas, and FicTrac ball tracking.

Developed NWB conversion tools for the Jazayeri lab's primate neurophysiology datasets studying working memory and mental navigation. The conversion pipeline handles Neuropixels and V-Probe recordings from frontal and entorhinal cortex, aligned to eye tracking, joystick, and task events.

Developed comprehensive NWB conversion tools for the Stavisky lab's brain-to-text decoding datasets. The conversion pipeline handles complex neural decoding data including RNN decoder outputs, language model predictions, and processed electrophysiology signals. Created custom visualization widgets for analyzing decoding performance, trial-aligned data, and temporal evolution of phoneme and word predictions. The tools support Redis-based data streaming and include extensive configuration options through YAML files.

Developed NWB conversion tools for the Datta lab's behavioral neuroscience datasets, featuring photometric recordings and optogenetic manipulations in mice. The conversion pipeline handles multi-modal data including fiber photometry signals, behavioral measurements, and closed-loop optogenetic stimulation data studying dopamine dynamics during spontaneous behavior.

Developed comprehensive NWB conversion tools for the Pinto lab's two-photon imaging datasets. The conversion pipeline handles Bruker Ultima microscope data, Suite2P segmentation outputs, and holographic stimulation experiments. Created a custom NWB extension (ndx-pinto-metadata) for storing ViRMEN experimental metadata, and the tools support both command-line and interactive notebook-based workflows for data conversion and analysis.

Developed NWB conversion tools for the Tye lab's valence experiments in mice, covering Open Ephys and Neuropixels electrophysiology, Miniscope calcium imaging, fiber photometry, behavioral video, and DeepLabCut and SLEAP pose estimation. The data behind the neurotensin study and the amygdalostriatal transition zone study are published on the DANDI Archive.

Developed NWB conversion tools for the Shuler lab's electrophysiology and behavioral datasets. The conversion pipeline integrates SpikeGLX recordings with behavioral event data, including specialized tools for data synchronization and cloud-based spike sorting workflows. The tools support comprehensive metadata handling through standardized JSON and CSV formats.

Developed NWB conversion tools for the Murthy lab's Drosophila courtship data from Cowley et al. (2024). The conversion combined courtship videos, pose tracks stored with ndx-pose, song recordings and labels from males with silenced visual projection neurons, and two-photon calcium imaging of those neurons in head-fixed flies viewing visual stimuli.

Developed NWB conversion tools for the Ahrens lab's whole-brain calcium imaging data in zebrafish. The project includes conversion of complex behavioral and neural recording datasets, including studies of glia-neuron interactions and behavioral state transitions. The data pipeline handles multi-modal integration of calcium imaging, behavioral measurements, and experimental metadata.

Developed NWB conversion tools for the Seidemann lab's two-photon imaging of macaque primary visual cortex during passive fixation. The conversion combines the raw imaging, Suite2p segmentation, and a custom interface for the task trials, eye tracking, and events in a single NWB file.

Developed NWB conversion tools for two Fee lab datasets: calcium imaging in mice from a lightweight head-mounted microscope with EXTRACT segmentation, and Neuropixels recordings from the zebra finch caudomedial nidopallium during song motif playback.

Developed NWB conversion tools for the Froemke lab's studies of maternal behavior in mice, covering two-photon imaging and whole-cell recordings from auditory cortex (Schiavo et al., 2020) and electrophysiology and fiber photometry from the paraventricular nucleus of co-housed virgin females (Carcea et al., 2021).

Developed software allowing the Kato lab to convert functional and structural volumetric imaging of the C. elegans nervous system to NWB, including extensions for Micro-Manager metadata and multi-channel volumetric data, and interactive visualizations for validating the converted files.

Developed NWB conversion tools for three of the O'Connor lab's datasets on whisker touch, cross-modal sensory selection, and sequence licking, converting the lab's MATLAB session format to NWB and publishing the results on DANDI.

Developed spike sorting pipelines and NWB conversion tools for the Brody lab's rat electrophysiology. SpikeInterface notebooks cover SpikeGLX Neuropixels, SpikeGadgets wireless tetrode, and Neuralynx tetrode recordings, and three converters combine these recordings with the lab's trial data and sorted units, including sessions from the Poisson clicks task.

Developed NWB conversion tools for the Feldman lab's neurophysiology datasets studying sensory processing in the somatosensory system. The conversion pipeline handles complex data structures from electrophysiological recordings and behavioral measurements, with specialized interfaces for processing neural activity during sensory stimulation tasks.

Developed NWB conversion tools for the Shenoy lab's reaching experiments in rhesus monkeys, covering a center-out task recorded with Utah arrays, Neuropixels recordings during an instructed-delay task, and the maze task. The center-out and maze datasets are published on the DANDI Archive, with a notebook and custom widget for viewing them.

Developed comprehensive NWB conversion tools for the Movshon lab's diverse electrophysiology and visual neuroscience datasets. The conversion pipeline handles multiple data formats including Blackrock, OpenEphys, and SpikeGLX recordings, with integrated spike sorting through SpikeInterface. The tools support both command-line and graphical user interface workflows, enabling efficient processing of complex visual neuroscience experiments. The project facilitates the standardization of the lab's extensive visual cortex recordings, supporting their research into neural mechanisms of visual perception and motion processing.

Developed NWB conversion tools for the Brunton lab's human neurobehavioral datasets, including the AJILE12 dataset featuring synchronized intracranial neural recordings and upper body pose trajectories. The conversion pipeline handles complex behavioral data including reach events, position tracking, and long-term naturalistic recordings spanning multiple modalities.

Developed NWB conversion tools for the Tank lab's behavioral and electrophysiology datasets. Created a custom NWB extension (ndx-tank-metadata) for storing experiment-specific metadata including maze configurations and rig parameters. The conversion pipeline integrates Neuropixels recordings with VirMen behavioral data, including detailed trial structure, behavioral metrics, and synchronized TTL events. The tools support extensive metadata handling and include specialized visualization widgets for behavioral analysis.

Developed NWB conversion tools for the International Brain Lab's standardized decision-making experiments, including custom NWB extensions for specialized data types. The conversion pipeline handles Neuropixels recordings, spike sorting, and behavioral data from multiple research sites, integrating wheel movements, video, pose estimation, and visual stimulation data across a large-scale collaboration.

Developed utilities for the Allen Institute's Visual Coding Neuropixels NWB files: a script that repairs session files so they open with PyNWB, and the hdf5zarr package for reading NWB files stored in the cloud through Zarr.

Developed NWB conversion tools for the Chang lab's high-density electrocorticography (ECoG) recordings in human patients. The project includes conversion of 256-channel neural recordings during speech production, with detailed annotations of speech events and anatomical electrode labels, demonstrating the capability to handle complex human neurophysiology data while maintaining HIPAA compliance.

Developed the ndx-simulation-output extension for storing large-scale simulation output from the Soltesz lab's NeuroH5 software, and began a conversion of Scanbox two-photon imaging and treadmill data.

Developed NWB conversion tools for the Buzsáki lab's extensive neurophysiology datasets, handling terabyte-scale data including Neuroscope recordings, LFP signals, and behavioral measurements. The conversion pipeline features specialized interfaces for various data types and supports parallel processing for large-scale conversions, with datasets publicly available through DANDI.

Developed NWB conversion tools for the Jaeger lab's motor cortex and thalamus experiments in mice, covering Intan electrophysiology, treadmill, LabVIEW, and Bpod behavior, optogenetic stimulation, and FRET imaging, with the ndx-fret extension.

Developed NWB conversion tools for the Buffalo lab's multi-modal neurophysiology data, handling both raw and processed neural recordings from Neuralynx systems, sorted spikes, and behavioral measurements in non-human primates doing hippocampal tasks. The conversion pipeline includes a graphical interface for metadata editing and supports various data formats including NCS, MAT, and NEX files.

Developed NWB conversion tools for the Giocomo lab's spatial navigation datasets, including tetrode and Neuropixels recordings from medial entorhinal cortex, and two-photon calcium imaging from hippocampal CA1. The conversion pipeline handles multi-modal data including neural recordings, virtual reality behavior, and head motion measurements.

Developed NWB conversion tools for the Axel lab's whole-brain two-photon calcium imaging in Drosophila, recorded with ball motion and tracked body positions. The pipeline converts raw volumes from MATLAB files and processed results from NumPy files, and includes a graphical interface for editing metadata and viewing the result with NWB Widgets.

Developed nwbpkg with the Schnitzer lab, a MATLAB package built on MatNWB that writes cell extraction outputs from CELLMax, EXTRACT, CNMF, CNMF-E, and PCA-ICA to NWB. We also wrote the ndx-extract extension to store the configuration of an EXTRACT run.