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@catalystneuro

CatalystNeuro

README.md

Data engineering for neuroscience labs 🧠

Neuroscience data is becoming larger and more complex everyday. The data we collect and the software we write can often be valuable outside the scope of the original project, and should be shared as public resources for the neuroscience community, but this is often a high bar for neuroscience labs to acheive on their own. While the benefits of sharing data and software are clear, it can be difficult for neroscientists to handle the data engineering challenges while focusing on the science.

We integrate with BRAIN Initiative-funded neuroinformatics projects such as the Neurodata Without Borders data standard, the DANDI Archive, and SpikeInterface to help labs adopt these tools. Our goal is to help labs share their data and software easily and effectively, and to facilitate secondary analysis of these datasets to accelerate the rate of scientific discovery. We believe that effective packaging and sharing of data and software will lead to new scientific workflows that build upon and combine existing studies, enabling deeper understanding of the brain and more rapid discovery of treatment for neurological disorders.

About Us 🧑‍💻

CatalystNeuro is a software consulting company that specializes in data engineering for neuroscience labs. We are a globally distributed team of neuroscientists who are also software developers, and we care deeply about helping neuroscience adopt state-of-the-art data engineering tools. We excel at helping data infrastructure tools with outreach and with helping neuroscience labs adopt data infrastructure tools, bridging the gap between developers and users. See our team here.

Key Software Projects 📈

  • NeuroConv automates conversion of data from common formats into the Neurodata Without Borders (NWB) format for distribution on the DANDI Archive.
  • NWB Widgets provides automatic, interactive visualizations of the data within NWB files that are scalable and integrated with the DANDI Archive.
  • SpikeInterface is a community-driven unified framework for spike sorting.
  • NWB GUIDE provides a user-friendly no-code graphical user interface for converting data to NWB, inspecting NWB files, and exploring the data within NWB files.

Links 🔗

You can find more information about us at the following links:

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  1. neuroconv neuroconv Public

    Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

    Python 46 22

  2. roiextractors roiextractors Public

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

    Python 11 6

  3. ecogVIS ecogVIS Public

    Time series visualizer and data processing tools for Electrocorticography (ECoG) signals stored in NWB files, for Python.

    Python 24 18

  4. lazy_ops lazy_ops Public

    Lazy transposing and slicing of h5py and Zarr Datasets

    Python 3 3

  5. cookiecutter-my-lab-to-nwb-template cookiecutter-my-lab-to-nwb-template Public

    The standard cookiecutter template for all lab-specific NWB conversions.

    Python 1 1

Repositories

Showing 10 of 178 repositories
  • ndx-binned-spikes Public

    NWB extension to store binned spikes with respect to an event (e.g. a non averaged PSTH)

    catalystneuro/ndx-binned-spikes’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Jul 13, 2024
  • dicarlo-lab-to-nwb Public
    catalystneuro/dicarlo-lab-to-nwb’s past year of commit activity
    Python 0 MIT 1 0 1 Updated Jul 13, 2024
  • GuPPy Public Forked from LernerLab/GuPPy

    Guided Photometry Analysis in Python, a free and open-source FP analysis tool.

    catalystneuro/GuPPy’s past year of commit activity
    Python 0 GPL-3.0 11 0 0 Updated Jul 12, 2024
  • vame-desktop Public

    A desktop application for the Variational Animal Motion Encoding project.

    catalystneuro/vame-desktop’s past year of commit activity
    TypeScript 2 GPL-3.0 0 8 0 Updated Jul 12, 2024
  • ndx-microscopy Public

    An enhancement to core NWB schema types related to microscopy data.

    catalystneuro/ndx-microscopy’s past year of commit activity
    Python 0 MIT 0 8 5 Updated Jul 12, 2024
  • lerner-lab-to-nwb Public
    catalystneuro/lerner-lab-to-nwb’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Jul 12, 2024
  • ndx-extracellular-channels Public
    catalystneuro/ndx-extracellular-channels’s past year of commit activity
    0 0 1 1 Updated Jul 12, 2024
  • higley-lab-to-nwb Public

    NWB Conversion project for the Higley lab

    catalystneuro/higley-lab-to-nwb’s past year of commit activity
    Python 0 MIT 0 4 2 Updated Jul 12, 2024
  • neuroconv Public

    Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

    catalystneuro/neuroconv’s past year of commit activity
    Python 46 BSD-3-Clause 22 94 33 Updated Jul 11, 2024
  • dandi_s3_log_parser Public

    S3 log parsing for the DANDI Archive.

    catalystneuro/dandi_s3_log_parser’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Jul 11, 2024
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