Repositories list

• 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•21•2•Updated Mar 13, 2025Mar 13, 2025

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•25•48•4•Updated Mar 13, 2025Mar 13, 2025

• aind-data-schema-models

  Public
  Data models used in aind-data-schema

  Python

  •

  MIT License

  •3•0•6•0•Updated Mar 13, 2025Mar 13, 2025

• aind-analyisis-wrapper

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

  Dockerfile

  •

  MIT License

  •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• aind-smartspim-data-transformation

  Public
  Data transformations applied to the SmartSPIM data before uploading to the cloud storage service.

  Python

  •

  MIT License

  •0•0•2•0•Updated Mar 12, 2025Mar 12, 2025

• metadata-chatbot

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

  metadata-chatbot

  Python

  •

  MIT License

  •0•2•10•0•Updated Mar 12, 2025Mar 12, 2025

• aind-smartspim-quantification

  Public
  Takes the output of segmentation and ccf registration to calculate cell counts per brain region

  Python

  •

  MIT License

  •2•1•4•0•Updated Mar 12, 2025Mar 12, 2025

• aind-metadata-mapper

  Public
  Repository to help gather and map metadata from different sources

  aind-data-infrastructure

  Python

  •

  MIT License

  •2•0•31•5•Updated Mar 12, 2025Mar 12, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•100•12•Updated Mar 12, 2025Mar 12, 2025

• aind-data-transfer-service

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

  aind-data-infrastructure

  Python

  •

  MIT License

  •0•3•14•1•Updated Mar 12, 2025Mar 12, 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 Mar 12, 2025Mar 12, 2025

• parallax

  Public
  GUI control software for the Modular Insertion System (MIS)

  processingacquisitionunder-development

  Python

  •

  MIT License

  •1•5•8•2•Updated Mar 12, 2025Mar 12, 2025

• Aind.Behavior.ExperimentLauncher

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

  aind-behavior

  Python

  •

  MIT License

  •0•0•12•3•Updated Mar 12, 2025Mar 12, 2025

• aind-ephys-ibl-gui-conversion

  Public
  convert ephys data for use in ibl gui

  Python

  •

  MIT License

  •1•0•0•1•Updated Mar 12, 2025Mar 12, 2025

• aind-SmartSPIM-segmentation

  Public
  segmentation module for SmartSPIM cloud pipeline

  Python

  •

  MIT License

  •1•2•1•0•Updated Mar 12, 2025Mar 12, 2025

• anivia

  Public
  Fork of VGG VIA to better support annotation of animal pose images

  JavaScript

  •

  BSD 2-Clause "Simplified" License

  •0•4•0•0•Updated Mar 12, 2025Mar 12, 2025

• aind-beh-ephys-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• aind-ephys-portal

  Public
  SpikeInterface GUI Portal

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•14•0•Updated Mar 12, 2025Mar 12, 2025

• aind-mri-utils

  Public
  Allen Institute for Neural Dynamics MRI utilities

  Python

  •

  MIT License

  •0•1•1•2•Updated Mar 12, 2025Mar 12, 2025

• aind-ephys-transformation

  Public
  Code to compress ephys data

  Python

  •

  MIT License

  •0•0•2•0•Updated Mar 12, 2025Mar 12, 2025

• aind-dynamic-foraging-qc

  Public
  Capsule for the QC of the dynamic foraging task

  Python

  •

  MIT License

  •0•0•1•1•Updated Mar 12, 2025Mar 12, 2025

• aind-file-standards

  Public
  MIT License

  •0•0•0•1•Updated Mar 12, 2025Mar 12, 2025

• aind-ephys-results-collector

  Public
  Code Ocean capsule for result collection

  Python

  •

  MIT License

  •0•0•1•0•Updated Mar 12, 2025Mar 12, 2025

• aind-analysis-arch-result-access

  Public
  accessing results from aind analysis architecture

  Jupyter Notebook

  •

  MIT License

  •0•0•1•0•Updated Mar 12, 2025Mar 12, 2025

• aind-metadata-service

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

  aind-data-infrastructure

  Python

  •

  MIT License

  •1•3•17•2•Updated Mar 12, 2025Mar 12, 2025

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•2•12•0•Updated Mar 12, 2025Mar 12, 2025

• aind-capsule-template

  Public template
  aind-core-servicesaind-data-infrastructure

  Dockerfile

  •

  MIT License

  •1•2•1•1•Updated Mar 11, 2025Mar 11, 2025

• Aind.Behavior.Telekinesis

  Public
  Task implemention of brain-computer interface experiments

  aind-behavior

  C#

  •

  MIT License

  •0•0•1•0•Updated Mar 11, 2025Mar 11, 2025

• Aind.Behavior.ForceForaging

  Public
  A repository for the aind-force-foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•1•5•0•Updated Mar 11, 2025Mar 11, 2025