Software Solutions

CatalystNeuro develops software solutions across the data pipeline aimed to help neuroscientists focus on the science and accelerate their discovery process immediately. We release and support packages for data homogenization, visualization, analysis, and lab-wide records. These libraries are developed by a team that focuses specifically on neural data and good software practices. Our projects are packaged, documented, and tested for robustness and ease of use. Everything we build is released as it is developed under a permissive license.

We commonly work with labs to customize these software solutions to the specific needs of the lab, interfacing our platforms with their data formats and analysis packages.

Analysis and Visualization Software

Our core projects allow us to develop software over the long term that meets needs that reoccur in the neurophysiology community.

ecogVlS Software Image

A GUI for electrophysiology data visualization, annotation, and preprocessing. ecogVlS was originally designed for the Chang Lab at UCSF to streamline preprocessing pipeline with the NWB data standard. The GUI is pure python which makes it hackable and easy to customize for specific applications. Graphing is performed by PyQtGraph, which is very performant.

NWBWidgets

A library of widgets for visualization of NWB data in a Jupyter notebook (or lab). The widgets allow you to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB files and to be easy to extend. This work is in collaboration with Kitware and has been funded in part by Kitware and the Allen Institute SBIR project.

SegmentationExtractors

Python-based module for extracting converting, and handling recorded optical imaging data from between different file formats. Inspired by the SpikeInterface project.

lazy_ops

Lazy transposing and slicing for h5py Datasets. Slice and transpose h5py Datasets lazily so that you can efficiently read only the data you need.

NWB Extensions

Neurodata Extensions (NDX) allow labs to standardize, share, and publish data outside of the core scope of NWB inside NWB files. We regularly build extensions to support unique data types and use-cases within cellular neurophysiology.

Simulation Output Software Image

This extension defines two NWB neuorodata_types, CompartmentSeries and Compartments. CompartmentSeries stores continuous data (e.g. membrane potential, calcium concentration) from many compartments of many cells, and scales to hundreds of thousands of compartments. Compartments stores the meta-data associated with those compartments, and is stored in SimulationMetaData. Compatibility with SONATA. Collaboration with Stanford University and the Allen Institute. Funded by the Ripple U19.

Bipolar Scheme Software Image

Structure for storing the bipolar schema of a recording in NWB file. Allows for storage of bipolar recordings, stimulation configurations, or offline bipolar re-referencing. Also allows for multiple electrodes to be combined into a single anode or cathode. Collaboration with the Chang Lab, UC San Francisco.

Point Cloud Table Software Image

Stores point cloud data in NWB. This can be used to track the shape of an animal over time. PointCloudTable inherits from DynamicTable, and can store an entire session of point cloud data in 4 datasets. Collaboration with Kitware Inc and the Soltesz Lab, Stanford University. Funded by the Ripple U19.

FRET Software Image

NWB extension for storing Fluorescence Resonance Energy Transfer (FRET) experimental data. A collaboration with Jaeger Lab, Emory University and The Kavli Foundation.

Lab-specific Repositories

Building lab-specific repositories allow us to customize our general tools for each lab’s specific use-case, and to showcase how that lab can use those tools to interface with their existing data and analysis.

Tollas and Brens

Tols-lc-to-nwb: Convert patch-master mat intracellular electrophyslology to NWB. Developed in collaboration with the Tolias and Berens lobs under the DANDI project

Dieter Jaeger, Emory University

jaeger-lab-data-to-nwb: Convert FRET optical imaging, extracellular electrophysiology, nad behavior. Funded by Kavil Foundation

Gyorgy Buzsaki, NYU

buzsoki-lob-to-nwb: Convert extracellulor electrophyslology and behavior, Funded by Stanford University, NIH as part of the Ripple U19.

Richard Axel, Columbia University

axe-Lab-to-nwb: NWB conversion scripts and tutorials for SCAPE microscopy data. Funded by Simons Foundation

Lisa Giocomo, Stanford University

giocomo-lab-to-nwt: Scripts and tutorials for converting SpikeGLX neuropixel extrocellular electrophyslology data to NWB. Wicludes demonstration of applying Spikelnteiface for spike-sorting.Funded by Simons Foxidation

Beth Buffalo, University of Washington

buffalo-lab-to-nwb: Scripts which convert Buffalo lab data to NWB format. Currently we only support conversion for processed data Funded by the Simons Foundation.

Contributions:

We are major contribution to the following repositories: