Repositories list

• aind-ephys-preprocessing

  Public
  CodeOcean capsule for ephys preprocessing

  Python

  •

  MIT License

  •55 forks•22 stars•44 issues•00 pull requests•Updated Oct 10, 2026Oct 10, 2026

• pinpoint

  Public

  AllenNeuralDynamics/pinpoint’s past year of commit activity
  Next-generation in vivo electrophysiology planning and automation tool.

  TypeScript

  •

  MIT License

  •00 forks•44 stars•1010 issues•00 pull requests•Updated Oct 10, 2026Oct 10, 2026

• rachel-analysis-utils

  Public

  AllenNeuralDynamics/rachel-analysis-utils’s past year of commit activity
  rachel's analysis utils for AIND-analysis-framework instances.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•22 pull requests•Updated Oct 10, 2026Oct 10, 2026

• aind-metadata-upgrader

  Public
  Upgrade JSON metadata from old versions of aind-data-schema

  Python

  •

  MIT License

  •33 forks•11 star•11 issue•00 pull requests•Updated Oct 10, 2026Oct 10, 2026

• harp.device.quac

  Public
  0364: This repository contains the hardware, firmware, and software related to the Harp quad DAC

  harp

  harp

  C#

  •

  MIT License

  •00 forks•00 stars•2323 issues•00 pull requests•Updated Oct 10, 2026Oct 10, 2026

• aind-software-docs

  Public

  AllenNeuralDynamics/aind-software-docs’s past year of commit activity
  Centralized documentation repository for Scientific Computing, publishes to RTD

  JavaScript

  •

  MIT License

  •00 forks•11 star•4343 issues•1010 pull requests•Updated Oct 10, 2026Oct 10, 2026

• ibl-ephys-alignment-gui

  Public
  Tool for aligning electrophysiological features to anatomical landmarks

  Python

  •

  MIT License

  •1919 forks•1212 stars•44 issues•00 pull requests•Updated Oct 10, 2026Oct 10, 2026

• aind-ephys-ibl-gui-conversion

  Public
  convert ephys data for use in ibl gui

  Python

  •

  MIT License

  •33 forks•00 stars•33 issues•22 pull requests•Updated Oct 10, 2026Oct 10, 2026

• zombie

  Public

  AllenNeuralDynamics/zombie’s past year of commit activity
  JavaScript

  •

  MIT License

  •11 fork•00 stars•2222 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •11 fork•22 stars•11 issue•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• brainwasher

  Public
  0354: control software for automated tissue clearing system

  Python

  •

  MIT License

  •11 fork•00 stars•1515 issues•88 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-motion-energy

  Public
  calculating motion energy (pixel luminance changes) from videos

  Python

  •

  MIT License

  •00 forks•11 star•44 issues•00 pull requests•Updated Oct 9, 2026Oct 9, 2026

• dynamic-foraging-task

  Public
  Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control

  Python

  •

  MIT License

  •77 forks•77 stars•11 issue•00 pull requests•Updated Oct 9, 2026Oct 9, 2026

• Aind.Behavior.Services

  Public
  A library for defining and maintaining behavior tasks.

  aind-behavior

  aind-behavior

  Python

  •

  MIT License

  •00 forks•11 star•22 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• aind-metadata-mapper

  Public
  Repository to help gather and map metadata from different sources

  aind-data-infrastructure

  aind-data-infrastructure

  Python

  •

  MIT License

  •22 forks•00 stars•3939 issues•33 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-dft-ephys-analysis

  Public
  shared library for dynamic foraging task (DFT) - neuropixels analysis

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-metadata-service

  Public
  REST API to compile metadata from various databases

  aind-data-infrastructure

  aind-data-infrastructure

  Python

  •

  MIT License

  •11 fork•33 stars•99 issues•00 pull requests•Updated Oct 9, 2026Oct 9, 2026

• biodata-cache

  Public
  Caching tools for storing expensive DocDB queries and S3 data tables in Redshift

  Python

  •

  MIT License

  •11 fork•00 stars•44 issues•66 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-docker-images

  Public
  aind-data-infrastructure

  aind-data-infrastructure

  Dockerfile

  •

  MIT License

  •00 forks•00 stars•33 issues•99 pull requests•Updated Oct 9, 2026Oct 9, 2026

• package-brain-atlas-assets

  Public
  Reorganize various brain atlas data assets into a standard organization and metadata convention.

  Python

  •

  MIT License

  •00 forks•00 stars•22 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• ophys-slap2-analysis

  Public
  Data reduction, preprocessing, and analysis for SLAP2 microscopes

  Jupyter Notebook

  •22 forks•33 stars•22 issues•22 pull requests•Updated Oct 9, 2026Oct 9, 2026

• one-liner

  Public
  adapter pattern implemented as zmq client/server

  sipe

  sipe

  Python

  •

  MIT License

  •00 forks•33 stars•2727 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• contraqctor

  Public
  A library for managing data contracts and quality control in behavioral datasets.

  aind-behavior

  aind-behavior

  Python

  •

  MIT License

  •11 fork•00 stars•99 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• openscope-community-predictive-processing

  Public
  This repository serves as a hub for community-driven contributions, documentation, and project tracking of the OpenScope Predictive Processing Community project…

  Python

  •

  MIT License

  •1313 forks•2727 stars•3232 issues•22 pull requests•Updated Oct 9, 2026Oct 9, 2026

• Aind.Experiment.VrForaging

  Public
  A repository to run VrForaging behavior experiments and compatible physiology platforms in AIND

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  aind-behavior

  C#

  •

  MIT License

  •00 forks•33 stars•77 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• aind-large-scale-cellpose

  Public
  Large-scale cell segmentation with cellpose.

  large-scalecell-segmentationzarr+ 3

  large-scalecell-segmentationzarrcellposeome-zarrcellpose-segmentation

  Python

  •

  MIT License

  •00 forks•1010 stars•44 issues•11 pull request•Updated Oct 9, 2026Oct 9, 2026

• aind-smartspim-classification

  Public
  Code for classifying the cell candidate outputs from aind-smartspim-segmentation within smartspim pipeline

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-ephys-pipeline

  Public
  AIND pipeline for processing extracellular electrophysiology data

  Nextflow

  •

  MIT License

  •1212 forks•4343 stars•1212 issues•33 pull requests•Updated Oct 9, 2026Oct 9, 2026

• aind-ephys-processing-qc

  Public
  CodeOcean Capsule for ephys quality control

  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2026Oct 9, 2026