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•27•0•Updated Oct 25, 2024Oct 25, 2024

• aind-metadata-entry-js

  Public
  Metadata entry using javascript

  aind-core-servicesaind-deploy-services

  JavaScript

  •

  MIT License

  •2•1•11•1•Updated Oct 25, 2024Oct 25, 2024

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•85•5•Updated Oct 25, 2024Oct 25, 2024

• aind-data-transfer-service

  Public
  FastAPI service to run data compression and transfer jobs on the hpc

  aind-core-servicesaind-deploy-services

  Python

  •

  MIT License

  •0•1•17•0•Updated Oct 25, 2024Oct 25, 2024

• thalamus-merfish-analysis

  Public
  Code Ocean capsule for sharing analysis of thalamus MERFISH data

  Jupyter Notebook

  •

  MIT License

  •1•2•2•0•Updated Oct 25, 2024Oct 25, 2024

• Aind.Behavior.ExperimentLauncher

  Public
  Source for for a minimal framework that can be used to build experimental interfaces

  Python

  •

  MIT License

  •0•1•4•0•Updated Oct 25, 2024Oct 25, 2024

• metadata-chatbot

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• aind-data-schema-models

  Public
  Data models used in aind-data-schema

  Python

  •

  MIT License

  •2•0•8•3•Updated Oct 25, 2024Oct 25, 2024

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•23•32•8•Updated Oct 25, 2024Oct 25, 2024

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•15•1•Updated Oct 25, 2024Oct 25, 2024

• 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 Oct 25, 2024Oct 25, 2024

• aind-ophys-utils

  Public
  Repo for Ophys utils

  Python

  •

  MIT License

  •0•0•35•2•Updated Oct 25, 2024Oct 25, 2024

• aind-data-transformation

  Public
  Library for basic data transformation requests such as compressing data or changing file formats

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•0•7•1•Updated Oct 25, 2024Oct 25, 2024

• aind-dynamic-foraging-basic-analysis

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

  Python

  •

  MIT License

  •0•0•8•1•Updated Oct 24, 2024Oct 24, 2024

• lamf-analysis

  Public
  Place for scientists & engineers on ophys-mFish projects (Learning mFISH, omFISH) to put ophys data processing development code, especially as a place to ease transition from LIMS to Codeocean

  Jupyter Notebook

  •

  MIT License

  •0•1•20•4•Updated Oct 24, 2024Oct 24, 2024

• aind-ophys-dff

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• aind-ophys-extraction-suite2p

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

  Python

  •

  MIT License

  •0•0•2•0•Updated Oct 24, 2024Oct 24, 2024

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •2•4•14•1•Updated Oct 24, 2024Oct 24, 2024

• aind-spot-get-multichannel

  Public
  Repository that takes the spots from a single channel and obtains statistics from other channels

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• nmcp-deploy

  Public
  Shell

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• Aind.Behavior.VrForaging.Analysis

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

  Jupyter Notebook

  •

  MIT License

  •0•0•4•0•Updated Oct 24, 2024Oct 24, 2024

• 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•4•0•Updated Oct 24, 2024Oct 24, 2024

• 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 Oct 24, 2024Oct 24, 2024

• 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•19•2•Updated Oct 24, 2024Oct 24, 2024

• view

  Public
  Model/View for exa-spim

  Python

  •1•3•10•1•Updated Oct 24, 2024Oct 24, 2024

• aind-session

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

  Python

  •

  MIT License

  •0•0•1•0•Updated Oct 24, 2024Oct 24, 2024

• aind-smartspim-template-dispatch

  Public
  This capsule only generates the configuration files necessary to divide the jobs in the cluster.

  Dockerfile

  •

  MIT License

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• aind-z1-spot-detection

  Public
  Scripts to detect spots on Z1 data

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• exaspim-control

  Public
  Python

  •

  MIT License

  •0•1•3•2•Updated Oct 24, 2024Oct 24, 2024