SCGB NWB Adoption

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 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 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 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 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 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 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 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 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.