Repositories list

• 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 Feb 7, 2025Feb 7, 2025

• aind-SmartSPIM-segmentation

  Public
  segmentation module for SmartSPIM cloud pipeline

  Python

  •

  MIT License

  •1•2•1•0•Updated Feb 7, 2025Feb 7, 2025

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•12•0•Updated Feb 7, 2025Feb 7, 2025

• dynamicrouting-encoding-fit

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• dynamicrouting-encoding-io

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• Aind.Behavior.Device.Olfactometer

  Public
  A repository for calibration and configuration of the harp olfactometer device

  aind-behavior

  C#

  •

  MIT License

  •0•0•4•0•Updated Feb 7, 2025Feb 7, 2025

• aind-ephys-curation

  Public
  Code Ocean capsule for ephys curation

  Python

  •

  MIT License

  •0•1•0•1•Updated Feb 7, 2025Feb 7, 2025

• aind-smartspim-pipeline

  Public
  Repository that hosts the SmartSPIM pipeline code

  Nextflow

  •

  MIT License

  •1•2•1•0•Updated Feb 7, 2025Feb 7, 2025

• iGluSnFR-simulation

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Feb 7, 2025Feb 7, 2025

• aind-units-nwb

  Public
  Code Ocean capsule to export ephys units data to NWB

  Python

  •

  MIT License

  •0•0•2•0•Updated Feb 7, 2025Feb 7, 2025

• aind-ecephys-nwb

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• aind-ephys-processing-qc

  Public
  CodeOcean Capsule for ephys quality control

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•103•9•Updated Feb 7, 2025Feb 7, 2025

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•1•14•2•Updated Feb 7, 2025Feb 7, 2025

• aind-metadata-service

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

  aind-data-infrastructure

  Python

  •

  MIT License

  •1•3•14•1•Updated Feb 7, 2025Feb 7, 2025

• exaspim-control

  Public
  Python

  •

  MIT License

  •2•1•0•0•Updated Feb 7, 2025Feb 7, 2025

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

  Public
  Python

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• coherent-lasers

  Public
  Python drivers for coherent lasers

  Python

  •

  MIT License

  •2•0•0•0•Updated Feb 7, 2025Feb 7, 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 7, 2025Feb 7, 2025

• Aind.Behavior.Services

  Public
  A repository containing code for data acquisition and processing for AIND behavior rigs.

  aind-behavior

  Python

  •

  MIT License

  •0•0•6•1•Updated Feb 7, 2025Feb 7, 2025

• thalamus-merfish-analysis

  Public
  Code Ocean capsule for sharing analysis of thalamus MERFISH data

  Jupyter Notebook

  •

  MIT License

  •1•2•2•0•Updated Feb 6, 2025Feb 6, 2025

• harp.device.sniff-detector

  Public
  Signal conditioning board for an implanted thermistor

  harp

  C#

  •

  MIT License

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

• harp.device.white-rabbit

  Public
  0361: A 16-output Harp clock synchronizer

  harp

  C#

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

• harp.core.pico

  Public
  A Harp core implementation on the RP2040

  harp

  C++

  •

  MIT License

  •0•4•18•0•Updated Feb 6, 2025Feb 6, 2025

• aind-multiplane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•3•1•Updated Feb 6, 2025Feb 6, 2025

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

  Public
  Nextflow

  •

  MIT License

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

• aind_data_schema_embeddings

  Public
  Embeddings of aind-data-schema codebase for GAMER RAG database

  metadata-chatbot

  Python

  •

  MIT License

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

• Aind.Behavior.VrForaging

  Public
  Task implemention of VR Foraging experiment

  aind-behavior

  C#

  •

  MIT License

  •0•2•12•0•Updated Feb 6, 2025Feb 6, 2025

• lc_analysis_demonstration

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025