Repositories list

• 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 15, 2025Jan 15, 2025

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•14•0•Updated Jan 15, 2025Jan 15, 2025

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

  Public
  Nextflow

  •

  MIT License

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

• aind-dynamic-foraging-data-utils

  Public
  Tools for the analysis of behavior and neural data from the dynamic foraging task

  Python

  •

  MIT License

  •0•2•23•0•Updated Jan 15, 2025Jan 15, 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 15, 2025Jan 15, 2025

• dynamicrouting-processing-template

  Public template
  Template for capsules that process one or all NWB files in an attached "datacube" asset

  Python

  •

  MIT License

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

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•23•52•7•Updated Jan 14, 2025Jan 14, 2025

• aind-data-asset-indexer

  Public
  aind-core-servicesaind-deploy-services

  Python

  •

  MIT License

  •0•0•10•1•Updated Jan 14, 2025Jan 14, 2025

• aind_su_etal_2022

  Public
  Migrated code from matlab to Python in su_etal_2022

  Python

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•1•9•0•Updated Jan 14, 2025Jan 14, 2025

• aind-data-access-api

  Public
  Library to interface with AIND databases

  aind-core-services

  Python

  •

  MIT License

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

• ephys-sorting-manual-curation

  Public
  Repository for collecting manual curation data for spike-sorting

  Python

  •0•1•0•0•Updated Jan 14, 2025Jan 14, 2025

• exaspim-control

  Public
  Python

  •

  MIT License

  •1•1•3•0•Updated Jan 14, 2025Jan 14, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•13•0•Updated Jan 14, 2025Jan 14, 2025

• aind-ephys-curation

  Public
  Code Ocean capsule for ephys curation

  Python

  •

  MIT License

  •0•1•0•1•Updated Jan 14, 2025Jan 14, 2025

• aind-ecephys-nwb

  Public
  Code Ocean capsule to create an NWB file for Neuropixels data

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• aind-ephys-visualization

  Public
  CodeOcean capsule for ephys visualization

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• aind-ephys-spikesort-spykingcircus2

  Public
  CodeOcean capsule for ephys spike sorting with Spyking-CIRCUS 2

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• aind-ephys-spikesort-kilosort25

  Public
  CodeOcean capsule for ephys spike sorting with Kilosort2.5

  Python

  •

  MIT License

  •0•1•0•0•Updated Jan 14, 2025Jan 14, 2025

• aind-metadata-mapper

  Public
  Repository to help gather and map metadata from different sources

  aind-core-services

  Python

  •

  MIT License

  •2•0•22•0•Updated Jan 13, 2025Jan 13, 2025

• mfishtoolspy

  Public
  Tools to analysis mFISH data, including gene panel selection from reference dataset

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•1•0•Updated Jan 13, 2025Jan 13, 2025

• aind-foraging-behavior-bonsai-trigger-pipeline

  Public
  Python

  •

  MIT License

  •0•1•1•0•Updated Jan 13, 2025Jan 13, 2025

• aind-spurious-correlation

  Public
  statistical tools to mitigate spurious correlations

  Python

  •

  MIT License

  •0•0•1•0•Updated Jan 13, 2025Jan 13, 2025

• aind-multiplane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Jan 13, 2025Jan 13, 2025

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•2•18•1•Updated Jan 13, 2025Jan 13, 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 13, 2025Jan 13, 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 13, 2025Jan 13, 2025

• aind-ephys-processing-qc

  Public
  CodeOcean Capsule for ephys quality control

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• aind-software-docs

  Public
  Centralized documentation repository for Scientific Computing, publishes to RTD

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 12, 2025Jan 12, 2025