Repositories list

• HIPPIE

  Public
  High-dimensional Interpretation for Physiological Patterns in Intercellular Electrophysiology (HIPPIE), a cVAE framework designed for multimodal neuron classification and clustering by integrating extracellular action potential waveforms with spike-timing derived measurements.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •3•2•0•0•Updated Dec 6, 2025Dec 6, 2025

• mission_control

  Public
  Contains the full stack of braingeneers services as well as start/stop procedures.

  Python

  •0•1•0•0•Updated Dec 5, 2025Dec 5, 2025

• braingeneerspy

  Public
  Python package for Braingeneers data loading, analysis, and IoT.

  Python

  •

  MIT License

  •7•20•7•3•Updated Dec 5, 2025Dec 5, 2025

• SIMS

  Public
  SIMS: Scalable, Interpretable Models for Cell Annotation of large scale single-cell RNA-seq data

  Python

  •

  MIT License

  •9•10•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

• SpikeData

  Public
  Library for analyzing and manipulating spike time datasets.

  Python

  •

  MIT License

  •0•4•4•1•Updated Nov 26, 2025Nov 26, 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

• Kilosort_docker

  Public
  Python

  •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

• human_hippocampus

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•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•0•0•0•Updated Aug 21, 2025Aug 21, 2025

• Catalogger

  Public
  Python

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 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
  Attempt to run SIMS inference in the browser

  Python

  •1•2•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•2•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

• GcodeGoblin

  Public
  Tool to manipulate G-Code for heat embossing.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• cellxgene-ingest

  Public
  Download scRNASeq from CZ Cell x Gene Census upload to NRP S3 optimized for ML

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 18, 2024Sep 18, 2024

• search

  Public
  Prototype search engine for experiment object store

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Aug 13, 2024Aug 13, 2024

• mearec

  Public
  Playing around with MEArec temp/rec generation

  AGS Script

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• IOT_Education_Lab_on_Chip_Paper

  Public
  We wrote educational programs for remote IoT and local IoT outreach in Bolivia.

  Python

  •0•1•0•0•Updated May 14, 2024May 14, 2024

• things

  Public
  Infrastructure to manage in lab linux endpoints collecting data and uploading to the cloud

  JavaScript

  •

  Apache License 2.0

  •0•0•2•1•Updated Apr 23, 2024Apr 23, 2024

• piphys

  Public
  Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments

  C++

  •

  MIT License

  •4•19•1•0•Updated Feb 20, 2024Feb 20, 2024

• braingeneers-docker-images

  Public
  Repository for braingeneers docker images

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•0•Updated Jan 30, 2024Jan 30, 2024