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    92 repositories

    • mission_control

      Public
      Contains the full stack of braingeneers services as well as start/stop procedures.
      Python
      •0•1•0•0•Updated Mar 18, 2026Mar 18, 2026

    • ooi-control-scripts

      Public
      Control scripts for fluidic automation and microscopy for incubator-free culture devices
      Shell
      •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • ooi-paper-supplemental

      Public
      Data for incubator-free automated culture paper
      Python
      •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • microscopy-pipeline

      Public
      Pipeline components for microscopy post-processing and analysis
      Python
      •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • braingeneerspy

      Public
      Python package for Braingeneers data loading, analysis, and IoT.
      Python
      •
      MIT License
      •7•20•8•2•Updated Mar 13, 2026Mar 13, 2026

    • incubatormicroscopesupplement

      Public
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • cytoverse

      Public
      Search and display cells in foundation model embedding space
      Jupyter Notebook
      •
      MIT License
      •1•9•0•0•Updated Feb 24, 2026Feb 24, 2026

    • HIPPIE

      Public
      High-dimensional Interpretation for Physiological Patterns in Intercellular Electrophysiology (HIPPIE), a cVAE framework designed for multimodal neuron classifi…
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•5•0•0•Updated Feb 14, 2026Feb 14, 2026

    • SpikeCanvas-EphysPipeline

      Public
      IoT messaging-based workflow orchestration framework with containerized ephys analysis for high-density MEA data
      Python
      •1•3•3•0•Updated Feb 6, 2026Feb 6, 2026

    • Kilosort_docker

      Public
      Python
      •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • educationpaper_supplemental_microscope

      Public
      HTML
      •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • SpikeData

      Public
      Library for analyzing and manipulating spike time datasets.
      Python
      •
      MIT License
      •0•4•4•1•Updated Dec 15, 2025Dec 15, 2025

    • Catalogger

      Public
      Python
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • HD-MEA-NeuronTracking

      Public
      Static neuron tracking using HD-MEA recordings
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • SIMS

      Public
      SIMS: Scalable, Interpretable Models for Cell Annotation of large scale single-cell RNA-seq data
      Python
      •
      MIT License
      •9•11•1•0•Updated Dec 3, 2025Dec 3, 2025

    • AndrewsGengVoitiukEtAl_SourceCode

      Public
      Source Code for our MS "Optogenetic modulation of epileptiform activity in human brain tissue"
      Jupyter Notebook
      •0•3•0•0•Updated Dec 1, 2025Dec 1, 2025

    • Picroscope-firmwares

      Public
      C++
      •1•3•3•11•Updated Nov 19, 2025Nov 19, 2025

    • Human_Hippocampus_Supplement

      Public
      Supplemental figures and tables for manuscript
      0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

    • human_hippocampus

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•2•1•Updated Oct 7, 2025Oct 7, 2025

    • kilosort4

      Public
      Python
      •1•2•0•1•Updated Oct 2, 2025Oct 2, 2025

    • fluoroMicroscope_StageCO2Incubator

      Public
      STLs, STEP files for CAD of our fluorescent microscope and stage-top CO2 Incubator.
      0•1•0•0•Updated Aug 21, 2025Aug 21, 2025

    • braindance

      Public
      Making neural stimulation easier
      Python
      •
      GNU General Public License v3.0
      •2•6•0•0•Updated Jul 18, 2025Jul 18, 2025

    • feedback-organoid-platform

      Public
      Supplementary Material for: "A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring""
      Python
      •
      Other
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • rtsort-web

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • sims-web

      Public
      Single Cell Embedding via SIMS in the Browser
      Python
      •1•3•0•0•Updated Jun 13, 2025Jun 13, 2025

    • Protosequences

      Public
      Analysis code for our paper "Protosequences in brain organoids model intrinsic brain states"
      Jupyter Notebook
      •1•3•0•0•Updated May 19, 2025May 19, 2025

    • nwb-converter

      Public
      Python
      •0•1•0•0•Updated May 8, 2025May 8, 2025

    • midbrain_parkinsons

      Public
      Elliott's code for midbrain project
      Jupyter Notebook
      •3•1•0•0•Updated May 5, 2025May 5, 2025

    • nrp-base-image

      Public
      Dockerfile
      •0•0•0•1•Updated Apr 21, 2025Apr 21, 2025

    • neural-link-mice

      Public
      Repo for deep learning approach to correlating between Hengenlab mice neural activity and physical activity.
      Jupyter Notebook
      •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024