Repositories list

• 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 8, 2025Jan 8, 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 8, 2025Jan 8, 2025

• aind-beh-ephys-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• aind_ssm_hackathon

  Public
  UW/Allen hackathon for dynamical systems models of behavior+neural data

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jan 8, 2025Jan 8, 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•16•0•Updated Jan 8, 2025Jan 8, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•204•11•Updated Jan 8, 2025Jan 8, 2025

• metadata-chatbot

  Public
  LLM (Anthropic Claude) based chatbot that can query, ingest and summarize metadata in a conversational form

  Python

  •

  MIT License

  •0•1•3•0•Updated Jan 8, 2025Jan 8, 2025

• aind-slims-api

  Public
  AIND-specific access to data stored in SLIMS

  Python

  •

  MIT License

  •1•0•5•3•Updated Jan 7, 2025Jan 7, 2025

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•23•48•5•Updated Jan 7, 2025Jan 7, 2025

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•14•0•Updated Jan 7, 2025Jan 7, 2025

• aind-dynamic-foraging-basic-analysis

  Public
  compute behavioral metrics and generate basic plottings for the dynamic foraging task

  Python

  •

  MIT License

  •0•0•14•2•Updated Jan 7, 2025Jan 7, 2025

• aind-spot-spectral-unmixing

  Public
  A capsule library for spectrally unmixing spots detected in multichannel lightsheet miscroscopy experiments.

  Python

  •

  MIT License

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

• aind-fip-qc-raw

  Public
  a capsule to generate QC based on fip raw data asest

  Python

  •

  MIT License

  •0•0•1•0•Updated Jan 7, 2025Jan 7, 2025

• aind-data-schema-models

  Public
  Data models used in aind-data-schema

  Python

  •

  MIT License

  •2•0•4•2•Updated Jan 7, 2025Jan 7, 2025

• Aind.Behavior.WaterTuner

  Public
  A repository with a pipeline for automatic water calibration for animal experiments.

  MIT License

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

• aind-subject-nwb

  Public
  Python

  •

  MIT License

  •0•0•1•1•Updated Jan 7, 2025Jan 7, 2025

• exaspim-control

  Public
  Python

  •

  MIT License

  •1•1•3•0•Updated Jan 7, 2025Jan 7, 2025

• aind-behavior-curriculum

  Public
  Starter repository for behavior base primitives.

  Python

  •

  MIT License

  •0•0•11•0•Updated Jan 7, 2025Jan 7, 2025

• Aind.Behavior.VrForaging.Analysis

  Public
  A repository with analysis code for the aind-vr-foraging experiment

  Jupyter Notebook

  •

  MIT License

  •0•0•1•0•Updated Jan 7, 2025Jan 7, 2025

• aind-data-access-api

  Public
  Library to interface with AIND databases

  aind-core-services

  Python

  •

  MIT License

  •0•2•16•0•Updated Jan 7, 2025Jan 7, 2025

• Aind.Behavior.Pirouette

  Public
  A repository with source code for long-term, freely moving, electrophisiology recordings in mice

  aind-behavior

  PowerShell

  •

  MIT License

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• aind-smartspim-classification

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• AIND-ophys-mFISH-design-matrix

  Public
  Building design matrices for ophys-mFISH datasets from AIND

  Python

  •

  MIT License

  •0•0•0•1•Updated Jan 6, 2025Jan 6, 2025

• segmentation-skeleton-metrics

  Public
  A Python package for evaluating a predicted segmentation of neural arbors by using skeleton-based metrics. This tool detects topological mistakes (i.e. splits and merges) in a predicted segmentation by comparing it to a set of ground truth skeletons.

  pythonevaluation-metricsneuron-segmentation

  Python

  •

  MIT License

  •0•6•1•0•Updated Jan 6, 2025Jan 6, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•13•0•Updated Jan 6, 2025Jan 6, 2025

• TigerASI

  Public
  a lightweight python interface for ASI brand Tiger Controllers

  driverspim

  Python

  •

  MIT License

  •2•5•12•2•Updated Jan 6, 2025Jan 6, 2025

• view

  Public
  Model/View for exa-spim

  Python

  •3•4•11•1•Updated Jan 6, 2025Jan 6, 2025

• aind-harp-workshop-materials

  Public
  PowerShell

  •

  MIT License

  •0•1•0•0•Updated Jan 6, 2025Jan 6, 2025

• Aind.Behavior.GitHubActions

  Public
  A repository with reusable github actions

  aind-behavior

  MIT License

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• Bonsai.AllenNeuralDynamics

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

  bonsai-rxaind-behavior

  C#

  •

  Other

  •0•0•6•0•Updated Jan 6, 2025Jan 6, 2025