Repositories list

• aind-slims-api

  Public
  AIND-specific access to data stored in SLIMS

  Python

  •

  MIT License

  •1•0•5•2•Updated Jan 30, 2025Jan 30, 2025

• aind-ophys-utils

  Public
  Repo for Ophys utils

  Python

  •

  MIT License

  •0•0•35•2•Updated Jan 30, 2025Jan 30, 2025

• aind-metadata-service

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

  aind-data-infrastructure

  Python

  •

  MIT License

  •1•3•14•0•Updated Jan 30, 2025Jan 30, 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 Jan 30, 2025Jan 30, 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 30, 2025Jan 30, 2025

• aind-analysis-arch-2nd-order-dynamic-foraging-model-comparison

  Public
  A prototype second-order analysis for dynamic foraging behavior model comparison

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•13•0•Updated Jan 30, 2025Jan 30, 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 30, 2025Jan 30, 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 Jan 30, 2025Jan 30, 2025

• Aind.Behavior.ForceForaging

  Public
  A repository for the aind-force-foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•1•5•1•Updated Jan 30, 2025Jan 30, 2025

• aind-metadata-mapper

  Public
  Repository to help gather and map metadata from different sources

  aind-data-infrastructure

  Python

  •

  MIT License

  •2•0•25•1•Updated Jan 30, 2025Jan 30, 2025

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •4•4•13•0•Updated Jan 29, 2025Jan 29, 2025

• exaspim-control

  Public
  Python

  •

  MIT License

  •1•1•3•0•Updated Jan 29, 2025Jan 29, 2025

• aind-data-schema-embeddings

  Public
  Embeddings of aind-data-schema for GAMER

  metadata-chatbot

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•108•11•Updated Jan 29, 2025Jan 29, 2025

• Aind.Behavior.Pirouette

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

  aind-behavior

  C#

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• iGluSnFR-simulation

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Jan 29, 2025Jan 29, 2025

• CaImAn-Suite2p-Registeration

  Public
  Capsule to compare CaImAn & Suite2p with StripRegisteration

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• thalamus-merfish-analysis

  Public
  Code Ocean capsule for sharing analysis of thalamus MERFISH data

  Jupyter Notebook

  •

  MIT License

  •1•2•2•0•Updated Jan 29, 2025Jan 29, 2025

• aind-fip-qc-raw

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

  Python

  •

  MIT License

  •0•0•3•0•Updated Jan 29, 2025Jan 29, 2025

• iGluSnFR-ROI

  Public
  Summarize Bergamo Peaks

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jan 29, 2025Jan 29, 2025

• AIND-ophys-mFISH-GLM

  Public
  GLM for ophys-mFISH datasets from AIND

  Python

  •

  MIT License

  •0•0•6•1•Updated Jan 29, 2025Jan 29, 2025

• aind-dynamic-foraging-basic-analysis

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

  Python

  •

  MIT License

  •0•0•17•4•Updated Jan 29, 2025Jan 29, 2025

• aind-ephys-curation

  Public
  Code Ocean capsule for ephys curation

  Python

  •

  MIT License

  •0•1•0•1•Updated Jan 29, 2025Jan 29, 2025

• aind-ephys-results-collector

  Public
  Code Ocean capsule for result collection

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 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 29, 2025Jan 29, 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 29, 2025Jan 29, 2025

• aind-units-nwb

  Public
  Code Ocean capsule to export ephys units data to NWB

  Python

  •

  MIT License

  •0•0•2•0•Updated Jan 29, 2025Jan 29, 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 Jan 29, 2025Jan 29, 2025

• lc_analysis_demonstration

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025