Repositories list

• lamf_analysis_lims

  Public
  Dev site for testing analysis pipelines and qc for learning mFISH project. Anything related to 2p data (plus behavior and spatial transcriptomics)

  Jupyter Notebook

  •0•0•0•0•Updated Jan 18, 2025Jan 18, 2025

• aind-ophys-extraction-suite2p

  Public
  Combines cellpose and suite2p to extract sources, i.e. ROIs and their traces.

  Python

  •

  MIT License

  •0•0•3•0•Updated Jan 18, 2025Jan 18, 2025

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•23•49•10•Updated Jan 18, 2025Jan 18, 2025

• aind-multiplane-ophys-pipeline-without-splitting

  Public
  Nextflow

  •

  MIT License

  •0•0•1•1•Updated Jan 18, 2025Jan 18, 2025

• aind-exaspim-soma-detection

  Public
  A Python package for detecting somas in ExaSPIM image datasets. Includes tools for image preprocessing and deep learning-based classification and training.

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jan 18, 2025Jan 18, 2025

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•2•15•1•Updated Jan 18, 2025Jan 18, 2025

• Aind.Behavior.CookieCutter.Template

  Public
  A cookiecutter template for Aind.Behavior repositories

  aind-behavior

  Python

  •

  MIT License

  •0•0•2•0•Updated Jan 18, 2025Jan 18, 2025

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•1•9•0•Updated Jan 17, 2025Jan 17, 2025

• aind-fip-dff

  Public
  This capsule takes an input raw NWB file of fiber data and creates processed DFF traces

  Python

  •

  MIT License

  •0•0•5•0•Updated Jan 17, 2025Jan 17, 2025

• Aind.Behavior.DynamicForaging

  Public
  A repository for the Dynamic Foraging task.

  Python

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•103•8•Updated Jan 17, 2025Jan 17, 2025

• ROICaT

  Public
  Region Of Interest Classification and Tracking

  Python

  •

  GNU General Public License v3.0

  •7•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• dynamicrouting-encoding-io

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• Aind.Behavior.ForceForaging

  Public
  A repository for the aind-force-foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•1•5•1•Updated Jan 17, 2025Jan 17, 2025

• aind-data-schema-models

  Public
  Data models used in aind-data-schema

  Python

  •

  MIT License

  •2•0•7•3•Updated Jan 17, 2025Jan 17, 2025

• aind-watchdog-service

  Public
  Data staging service that prepares acquistion data for cloud upload to Amazon S3 and Code Ocean processing.

  Python

  •

  MIT License

  •1•2•18•1•Updated Jan 17, 2025Jan 17, 2025

• aind-multiplane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•4•0•Updated Jan 17, 2025Jan 17, 2025

• dynamicrouting-encoding-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•13•0•Updated Jan 17, 2025Jan 17, 2025

• aind-session

  Public
  User-friendly tools for accessing paths, metadata and assets related to AIND sessions

  Python

  •

  MIT License

  •0•0•2•0•Updated Jan 17, 2025Jan 17, 2025

• dynamicrouting-encoding-fit

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• harp.device.lickety-split

  Public
  an ephys-compliant capacitive lick detector

  harp

  C++

  •

  MIT License

  •0•0•20•0•Updated Jan 17, 2025Jan 17, 2025

• aind-ephys-rig-qc

  Public
  Post-experiment temporal alignment and quality control

  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• Aind.Behavior.GitHubActions

  Public
  A repository with reusable github actions

  aind-behavior

  MIT License

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• Aind.Behavior.VideoEncodingBenchmarks

  Public
  A repository with code for benchmarking online video acquisition/encoding pipelines

  aind-behavior

  C#

  •

  MIT License

  •0•0•2•0•Updated Jan 17, 2025Jan 17, 2025

• aind-codeocean-utils

  Public
  Repository to facilitate interfacing with Code Ocean's index

  Python

  •

  MIT License

  •0•0•5•1•Updated Jan 17, 2025Jan 17, 2025

• aind-metadata-service

  Public
  Service to retrieve Labtracks/Sharepoint info using a REST API

  aind-core-servicesaind-deploy-services

  Python

  •

  MIT License

  •1•3•15•1•Updated Jan 17, 2025Jan 17, 2025

• Bonsai.AllenNeuralDynamics

  Public
  A Bonsai package for version control and manipulation of Git repositories

  bonsai-rxaind-behavior

  C#

  •

  Other

  •0•0•7•0•Updated Jan 17, 2025Jan 17, 2025

• aind-ophys-roicat-session-matching

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•3•0•Updated Jan 16, 2025Jan 16, 2025

• aind-data-asset-indexer

  Public
  aind-core-servicesaind-deploy-services

  Python

  •

  MIT License

  •0•0•9•0•Updated Jan 16, 2025Jan 16, 2025