Repositories list

• aind-registration-utils

  Public
  Tools for registering volumes

  Python

  •

  MIT License

  •0•0•0•1•Updated Dec 4, 2024Dec 4, 2024

• aind-mri-targeting

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•0•7•0•Updated Dec 4, 2024Dec 4, 2024

• aind-ophys-bergamo-stitcher

  Public
  Converts all tiff files collected during acquitision into a single hdf5 file for ophys processing

  Python

  •

  MIT License

  •0•0•3•1•Updated Dec 4, 2024Dec 4, 2024

• aind-ophys-motion-correction

  Public
  Python

  •

  MIT License

  •0•1•10•1•Updated Dec 4, 2024Dec 4, 2024

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•5•131•5•Updated Dec 4, 2024Dec 4, 2024

• AIND-CNC-SmartSPIM-Workshop

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• aind_pose_tracking_pipeline_dispatcher

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•14•0•Updated Dec 3, 2024Dec 3, 2024

• aind-morphology-utils

  Public
  Python

  •

  MIT License

  •0•0•1•4•Updated Dec 3, 2024Dec 3, 2024

• harp.core.pico

  Public
  A Harp core implementation on the RP2040

  harp

  C++

  •

  MIT License

  •0•4•18•0•Updated Dec 3, 2024Dec 3, 2024

• metadata-chatbot

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

  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 3, 2024Dec 3, 2024

• aind-ophys-fov-summary-qc

  Public
  Python

  •

  MIT License

  •0•0•3•0•Updated Dec 3, 2024Dec 3, 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•15•1•Updated Dec 3, 2024Dec 3, 2024

• aind-analysis-arch-upload-db-s3

  Public
  upload results to docDB and s3

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

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

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• aind-metadata-mapper

  Public
  Repository to help gather and map metadata from different sources

  aind-core-services

  Python

  •

  MIT License

  •2•0•23•0•Updated Dec 3, 2024Dec 3, 2024

• aind-ephys-processing-qc

  Public
  CodeOcean Capsule for ephys quality control

  Python

  •

  MIT License

  •0•0•0•1•Updated Dec 3, 2024Dec 3, 2024

• voxel

  Public
  General purpose microscope control repository

  Python

  •

  MIT License

  •3•4•13•1•Updated Dec 3, 2024Dec 3, 2024

• aind-metadata-service

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

  aind-core-servicesaind-deploy-services

  Python

  •

  MIT License

  •1•3•21•2•Updated Dec 3, 2024Dec 3, 2024

• aind-subject-nwb

  Public
  Python

  •

  MIT License

  •0•0•1•1•Updated Dec 3, 2024Dec 3, 2024

• aind-dynamic-foraging-basic-analysis

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

  Python

  •

  MIT License

  •0•0•14•2•Updated Dec 2, 2024Dec 2, 2024

• aind-behavior-data-transformation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• aind-pophys-data-transformation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• exaspim-control

  Public
  Python

  •

  MIT License

  •0•1•3•0•Updated Dec 2, 2024Dec 2, 2024

• aind-mri-utils

  Public
  Allen Institute for Neural Dynamics MRI utilities

  Python

  •

  MIT License

  •0•0•1•0•Updated Dec 2, 2024Dec 2, 2024

• Aind.Behavior.CurriculumTemplate

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

  Python

  •

  MIT License

  •0•0•2•0•Updated Dec 1, 2024Dec 1, 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•0•Updated Nov 28, 2024Nov 28, 2024

• aind-exaspim-soma-detection

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• aind-behavior-video-transformation

  Public
  Library to manage compression and transformation of behavior videos

  Python

  •

  MIT License

  •0•0•2•0•Updated Nov 28, 2024Nov 28, 2024