Repositories list

• iGluSnFR-In-Vivo-MC-Evaluation

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•25•50•6•Updated Feb 26, 2025Feb 26, 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•15•0•Updated Feb 26, 2025Feb 26, 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 Feb 26, 2025Feb 26, 2025

• aind-file-standards

  Public
  MIT License

  •0•0•1•1•Updated Feb 26, 2025Feb 26, 2025

• supervoxel-loss

  Public
  Efficient connectivity-preserving loss function for training neural networks to perform instance segmentation.

  Python

  •

  MIT License

  •0•1•0•0•Updated Feb 26, 2025Feb 26, 2025

• aind-data-asset-indexer

  Public
  aind-data-infrastructure

  Python

  •

  MIT License

  •0•0•10•1•Updated Feb 26, 2025Feb 26, 2025

• Aind.Behavior.CurriculumTemplate

  Public
  A template of a repository to be used for defining, running and interfacing with a behavior curriculum

  aind-behavior

  Python

  •

  MIT License

  •0•0•2•0•Updated Feb 26, 2025Feb 26, 2025

• aind-behavior-curriculum

  Public
  Starter repository for behavior base primitives.

  Python

  •

  MIT License

  •0•0•13•0•Updated Feb 26, 2025Feb 26, 2025

• openscope-community-predictive-processing

  Public
  This repository stores bonsai scripts to replicate experiments that are part of the OpenScope predictive processing community project

  GLSL

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•100•9•Updated Feb 26, 2025Feb 26, 2025

• Aind.Behavior.DynamicForaging

  Public
  A repository for the Dynamic Foraging task.

  Python

  •0•0•1•1•Updated Feb 26, 2025Feb 26, 2025

• nicheformer_analysis

  Public
  Analysis capsule for nicheformer LC-NE data

  Dockerfile

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• 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•0•Updated Feb 26, 2025Feb 26, 2025

• aind-beh-ephys-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• nicheformer

  Public
  Repository for Nicheformer: a foundation model for single-cell and spatial omics

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •4•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• dynamic-routing-unit-drift-qc-dashboard

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• brain_observatory_utilities_ophys

  Public
  Analysis tools for SDK like

  Jupyter Notebook

  •

  Other

  •3•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• aind-registration-utils

  Public
  Tools for registering volumes

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•14•0•Updated Feb 25, 2025Feb 25, 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•11•2•Updated Feb 25, 2025Feb 25, 2025

• aind-data-migration-utils

  Public
  Helper functions to support data migration

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• aind-multiplane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•0•2•Updated Feb 25, 2025Feb 25, 2025

• harp.device.white-rabbit

  Public
  0361: A 16-output Harp clock synchronizer

  harp

  C#

  •0•1•1•0•Updated Feb 25, 2025Feb 25, 2025

• posetail

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Feb 25, 2025Feb 25, 2025

• aind-mri-targeting

  Public
  Scripts and useful functions to plan neuroscience experiments using structural MRIs

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• aind-data-schema-models

  Public
  Data models used in aind-data-schema

  Python

  •

  MIT License

  •2•0•6•0•Updated Feb 25, 2025Feb 25, 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•13•0•Updated Feb 25, 2025Feb 25, 2025

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•1•12•1•Updated Feb 25, 2025Feb 25, 2025

• segmentation-skeleton-metrics

  Public
  A Python package for evaluating the topological accuracy of a neuron segmentation by computing skeleton-based metrics.

  skeletonsevaluation-metricsneuron-segmentation+ 1flood-filling-networks

  Python

  •

  MIT License

  •0•6•1•0•Updated Feb 25, 2025Feb 25, 2025