Repositories list

• 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•14•1•Updated Dec 13, 2024Dec 13, 2024

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

  Public
  Nextflow

  •

  MIT License

  •0•0•1•0•Updated Dec 13, 2024Dec 13, 2024

• aind-ophys-decrosstalk-roi-images

  Public
  Python

  •

  MIT License

  •0•0•11•1•Updated Dec 13, 2024Dec 13, 2024

• scicomp-docs

  Public
  Centralized documentation repository for Scientific Computing, publishes to RTD

  Python

  •

  MIT License

  •0•0•2•0•Updated Dec 13, 2024Dec 13, 2024

• aind-data-schema

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

  aind-core-services

  Python

  •

  MIT License

  •17•23•53•6•Updated Dec 12, 2024Dec 12, 2024

• dynamic-foraging-task

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

  Python

  •

  MIT License

  •4•6•149•5•Updated Dec 12, 2024Dec 12, 2024

• aind-foraging-behavior-bonsai-basic

  Public
  Basic analyses of foraging behavior .nwb from Bonsai

  Jupyter Notebook

  •

  MIT License

  •0•0•8•0•Updated Dec 12, 2024Dec 12, 2024

• foraging-behavior-browser

  Public
  Foraging behavior browser (streamlit)

  Python

  •

  MIT License

  •2•2•14•0•Updated Dec 12, 2024Dec 12, 2024

• aind-fip-dff

  Public
  This capsule takes an input raw NWB file of fiber data and creates processed DFF traces

  Python

  •

  MIT License

  •0•0•7•0•Updated Dec 12, 2024Dec 12, 2024

• aind-qc-portal

  Public
  Quality control portal

  Python

  •

  MIT License

  •0•0•8•0•Updated Dec 12, 2024Dec 12, 2024

• dynamicrouting-processing-template

  Public template
  Template for capsules that process one or all NWB files in an attached "datacube" asset

  Python

  •

  MIT License

  •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• aind-ophys-motion-correction

  Public
  Python

  •

  MIT License

  •0•1•12•2•Updated Dec 12, 2024Dec 12, 2024

• aind-ephys-preprocessing

  Public
  CodeOcean capsule for ephys preprocessing

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• mfishtoolspy

  Public
  Tools to analysis mFISH data, including gene panel selection from reference dataset

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•1•0•Updated Dec 12, 2024Dec 12, 2024

• Aind.Behavior.CookieCutter.Template

  Public
  A cookiecutter template for Aind.Behavior repositories

  aind-behavior

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• aind-slims-api

  Public
  AIND-specific access to data stored in SLIMS

  Python

  •

  MIT License

  •1•0•5•2•Updated Dec 12, 2024Dec 12, 2024

• dynamicrouting-decoding

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 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•22•1•Updated Dec 12, 2024Dec 12, 2024

• aind-exaspim-soma-detection

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

• aind-single-plane-ophys-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

• aind-mri-utils

  Public
  Allen Institute for Neural Dynamics MRI utilities

  Python

  •

  MIT License

  •0•0•1•0•Updated Dec 12, 2024Dec 12, 2024

• aind-morphology-utils

  Public
  Python

  •

  MIT License

  •0•0•1•2•Updated Dec 11, 2024Dec 11, 2024

• 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 Dec 11, 2024Dec 11, 2024

• 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 Dec 11, 2024Dec 11, 2024

• aind-session

  Public
  User-friendly tools for accessing paths, metadata and assets related to AIND sessions

  Python

  •

  MIT License

  •0•0•2•0•Updated Dec 11, 2024Dec 11, 2024

• Aind.Behavior.Services

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

  aind-behavior

  C#

  •

  MIT License

  •0•0•11•3•Updated Dec 11, 2024Dec 11, 2024

• aind-ephys-processing-qc

  Public
  CodeOcean Capsule for ephys quality control

  Python

  •

  MIT License

  •0•0•0•1•Updated Dec 11, 2024Dec 11, 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 11, 2024Dec 11, 2024

• aind-analysis-arch-job-manager

  Public
  capsule that registers, triggers, and manages analysis jobs for aind-analysis-arch

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• AIND-ophys-mFISH-GLM

  Public
  GLM for ophys-mFISH datasets from AIND

  Python

  •

  MIT License

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