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.

Comprehensive data standardization services to convert existing Blackrock format neurophysiology datasets to the Neurodata Without Borders (NWB) format to enhance data interoperability and facilitate sharing. The project focuses on converting the DABI 'Generalized Click' dataset (dataset #31) and the MoveAgain dataset to NWB format with thorough dataset assessment, custom conversion script development, rigorous quality validation, and comprehensive documentation. The conversion process follows established methodology including examination of data structure and metadata content, development of custom conversion scripts utilizing NWB ecosystem expertise, validation testing to ensure data integrity, and preparation for potential DANDI Archive publication.

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 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 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.

Developed NWB conversion tools for the Suver lab's research on Drosophila sensorimotor integration. The pipeline standardizes behavioral data from multiple cameras, wing beat tracking from microphone or tachometer recordings, antenna position tracking via DeepLabCut, and patch clamp recordings through Nidaq. These tools enable comprehensive analysis of neural activity in relation to complex fly behaviors.

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 Schnitzer lab's in vivo calcium imaging datasets. The conversion pipeline handles data from miniaturized microscopes (miniscopes) and fiber photometry recordings, including behavioral measurements during freely moving animal experiments. The tools support both one-photon and two-photon calcium imaging data, with specialized interfaces for motion correction and cell segmentation outputs.

Developed NWB conversion tools for the Dickerson lab's research on Drosophila sensory processing. The pipeline standardizes two-photon imaging data from ThorLabs microscopes, neck muscle imaging, and high-speed video recordings. These tools integrate synchronization data from ThorSync to align neural and behavioral measurements, facilitating comprehensive analysis of sensory-motor transformations.

Developed NWB conversion tools for the Lin lab's neural recording datasets focused on social behavior and maternal care. The datasets include synchronized behavioral monitoring and neural recordings from the hypothalamic paraventricular nucleus (PVN), particularly examining oxytocin neurons during maternal behavior transmission between experienced mothers and virgin mice.

Developed NWB conversion tools for the Cohen lab's research on Drosophila behavior. The conversion pipeline standardizes high-resolution videos of behaving flies along with synchronized behavioral measurements stored in MATLAB formats. These tools enable researchers to correlate detailed fly movements with other physiological and sensory data.

Developed NWB conversion tools for the Losonczy lab's two-photon calcium imaging datasets. The conversion pipeline handles data from head-fixed mice running on voluntary treadmills, including raw ROI images, DfOverF traces, fluorescence traces, and behavioral measurements. The tools support molecular identification of interneuron subtypes and integrate position tracking with neural activity data.

Developed NWB conversion tools for the Fox lab's research on Drosophila sensory systems. The pipeline standardizes high-speed video recordings, DeepLabCut output files, confocal imaging data, and intracellular electrophysiology recordings. These tools integrate stimulus traces and synchronization signals from Spike2, enabling researchers to study sensory processing across multiple modalities with precisely aligned data.

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, handling complex multi-modal data including two-photon calcium imaging, holographic stimulation, and visual stimulus data. The conversion pipeline integrates sophisticated experimental protocols including retinotopy mapping, orientation tuning, and targeted stimulation of neuronal ensembles in primary visual cortex.

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 during locomotion. The conversion pipeline includes specialized interfaces for handling complex imaging data formats including NiFTI files, with support for brain-wide neural activity mapping during behavioral tasks.

Developed NWB conversion tools for the Jazayeri lab's primate neurophysiology datasets studying cognitive timing and mental navigation. The conversion pipeline handles complex neural recordings from multiple brain regions including dorsomedial frontal cortex and entorhinal cortex during sophisticated behavioral tasks.

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 neuroscience datasets, with a focus on neurotensin valence experiments. The conversion pipeline includes custom behavioral interfaces and comprehensive metadata handling through YAML configuration files. The tools support both pip-installable package distribution and development workflows for adapting to evolving experimental needs.

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 neuroscience datasets. The conversion pipeline handles complex behavioral and neural data, including calcium imaging of visual neurons during courtship behavior, processed SLEAP joint position tracks, and song labels, supporting research into neural circuits underlying social behavior in fruit flies.

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 neuroscience datasets. The conversion pipeline includes custom behavioral interfaces and supports multiple experimental paradigms. The tools provide both command-line and programmatic conversion workflows, with comprehensive metadata handling through YAML configuration files.

Developed NWB conversion tools for the Fee lab's neurophysiology datasets studying neural mechanisms of learning and behavior. The conversion pipeline supports complex data structures from electrophysiological recordings and behavioral measurements, with specialized interfaces for processing and analyzing neural activity patterns during behavioral tasks.

Developed NWB conversion tools for the Froemke lab's neurophysiology datasets studying auditory cortex plasticity and maternal behavior. The conversion pipeline handles complex data including neural recordings during vocalization processing, behavioral measurements, and oxytocin system manipulations, capturing both intrinsic and experience-dependent plasticity mechanisms.

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 the O'Connor lab's neuroscience datasets. The conversion pipeline integrates MATLAB-based data processing with Python-based NWB conversion workflows, enabling standardization of complex experimental data. The tools include specialized interfaces for handling MATLAB-generated data structures and converting them into the NWB format.

Developed NWB conversion tools for the Brody lab's neurophysiology datasets focused on decision-making and neural circuits. The project includes custom processing pipelines and utility code for converting experimental data to the standardized NWB format, with specialized Python-based conversion tools.

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 comprehensive NWB conversion tools for the Shenoy lab's diverse motor neuroscience datasets. The conversion pipeline handles multiple experimental paradigms including center-out reaching tasks, Neuropixels recordings in monkeys, and maze navigation tasks. Created analysis and visualization pipelines for examining neural population dynamics during reaching and delay activity in premotor cortex. The tools support both direct streaming from DANDI and local data conversion workflows.

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 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 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 comprehensive 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 multi-modal behavioral and neural data from multiple research sites, integrating wheel movements, video recordings, and visual stimulation data across a large-scale collaboration.

Developed NWB conversion tools and utilities for the Allen Institute's Neuropixels datasets. The project includes tools for handling simultaneous Neuropixels probe recordings and EEG data, along with cortical electrical stimulation in head-fixed mice. The conversion pipeline supports complex multi-modal experiments investigating brain states and cortico-thalamic interactions across different behavioral conditions.

Developed NWB conversion tools for the Soltesz lab's neuroscience datasets. The tools facilitate the standardization of experimental data into the NWB format, supporting the lab's research in neural circuit dynamics and computational neuroscience.

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 neuroscience datasets studying basal ganglia circuits. The conversion pipeline handles complex electrophysiology recordings and computational modeling data, with specialized interfaces for processing multi-channel recordings and analyzing neural dynamics in motor control circuits.

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 Neuropixel 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 neurophysiology data, featuring both raw and processed data conversion capabilities. The project includes a comprehensive conversion pipeline with GUI tools for metadata editing and data visualization, supporting multiple data formats including NPZ and MAT files.