Repositories list

• abc-merfish-analysis

  Public
  Shared tools for accessing and processing ABC Atlas MERSCOPE data.

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• aind-metadata-upgrader

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

  Python

  •

  MIT License

  •1•1•4•1•Updated Aug 6, 2025Aug 6, 2025

• aind-data-schema

  Public
  A library that defines AIND data schema and validates JSON.

  aind-core-services

  Python

  •

  MIT License

  •17•26•17•3•Updated Aug 6, 2025Aug 6, 2025

• aind-single-plane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•1•1•1•Updated Aug 6, 2025Aug 6, 2025

• aind-analysis-wrapper

  Public
  Capsule that serves a wrapper for running analysis functions on input data

  Jupyter Notebook

  •

  MIT License

  •1•0•2•1•Updated Aug 6, 2025Aug 6, 2025

• aind-analysis-pipeline-template

  Public
  Pipeline with job dispatch and analysis wrapper capsules that serves as template for analysis

  Nextflow

  •

  MIT License

  •0•0•1•0•Updated Aug 5, 2025Aug 5, 2025

• aind-analysis-job-dispatch

  Public
  Capsule to create the input job model for analysis wrapper

  Python

  •

  MIT License

  •0•0•2•1•Updated Aug 5, 2025Aug 5, 2025

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•2•30•1•Updated Aug 5, 2025Aug 5, 2025

• aind-nwb-utils

  Public
  Useful functions for reading and writing NWB files

  Python

  •

  MIT License

  •0•1•7•2•Updated Aug 5, 2025Aug 5, 2025

• analysis-pipeline-utils

  Public
  Utilities to facilitate writing scientific analysis pipelines to run in Code Ocean, in conjunction with S3 and DocumentDB storage

  Python

  •

  MIT License

  •0•0•2•0•Updated Aug 5, 2025Aug 5, 2025

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•3•12•2•Updated Aug 5, 2025Aug 5, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•26•7•Updated Aug 5, 2025Aug 5, 2025

• parallax

  Public
  Automatic detection of probe position from multiple camera views

  electrophysiologymachine-visionunder-development+ 1neuropixels

  Python

  •

  MIT License

  •1•5•7•2•Updated Aug 5, 2025Aug 5, 2025

• Bonsai.AllenNeuralDynamics

  Public
  A repository with Bonsai packages used in AIND

  bonsai-rxaind-behavior

  C#

  •

  Other

  •0•0•9•0•Updated Aug 5, 2025Aug 5, 2025

• 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

  •12•12•30•1•Updated Aug 5, 2025Aug 5, 2025

• aind-vr-forgaging-processing-nwb-packaging

  Public
  Capsule that packages processed data for vr foraging behavior task

  Jupyter Notebook

  •

  MIT License

  •0•0•3•0•Updated Aug 5, 2025Aug 5, 2025

• brainwasher

  Public
  0354: control software for automated tissue clearing system

  Python

  •

  MIT License

  •1•0•14•1•Updated Aug 5, 2025Aug 5, 2025

• aind-file-standards

  Public
  MIT License

  •0•0•3•3•Updated Aug 4, 2025Aug 4, 2025

• aind-data-access-api

  Public
  Library to interface with AIND databases

  aind-core-servicesaind-data-infrastructure

  Python

  •

  MIT License

  •0•2•8•1•Updated Aug 4, 2025Aug 4, 2025

• aind-analysis-arch-result-access

  Public
  accessing results from aind analysis architecture

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• aind-exaspim-neuron-segmentation

  Public
  A Python package for performing neuron segmentation in ExaSPIM image datasets.

  segmentation

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• aind-ephys-portal

  Public
  SpikeInterface GUI Portal

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• exaspim-control

  Public
  Python

  •

  MIT License

  •2•1•0•0•Updated Aug 4, 2025Aug 4, 2025

• aind-mri-utils

  Public
  Allen Institute for Neural Dynamics MRI utilities

  Python

  •

  MIT License

  •0•2•1•3•Updated Aug 4, 2025Aug 4, 2025

• aind-mri-targeting

  Public
  Scripts and useful functions to plan neuroscience experiments using structural MRIs

  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 4, 2025Aug 4, 2025

• Aind.Behavior.GitHubActions

  Public
  A repository with reusable github actions

  aind-behavior

  MIT License

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• FIP_DAQ_Control

  Public
  C++

  •

  MIT License

  •0•0•4•1•Updated Aug 4, 2025Aug 4, 2025

• Aind.Behavior.IsoForce

  Public
  A repository for a joystick task

  C#

  •

  MIT License

  •0•0•2•1•Updated Aug 3, 2025Aug 3, 2025

• thalmanac

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•13•0•Updated Aug 2, 2025Aug 2, 2025