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Minicourse EDDA-QF21

Access large-scale free neuroimaging datasets using NeuroJSON.io website and REST-API

Qianqian Fang

About this course

NeuroJSON.io is an emerging new resource for all fNIRS researchers for sharing their study data as well as accessing large-scale standardized (BIDS, SNIRF among others) multi-modal neuroimaging data resources. NeuroJSON.io is easy to use, easy to search, with every hosted dataset easily accessible via REST-APIs in MATLAB and Python.

The goal of this mini-course is to give participants a hands-on tutorial on all key functionalities provided by the NeuroJSON.io website, and teach participants step-by-step how to query, download and analyze over BIDS-compatible measurement data from over 40,000 subjects in MATLAB and Python using easy to use REST-API.

Learning Outcomes

  • fNIRS researchers who want to share their research data with the broader communities
  • computational researchers in the neuroimaging and fNIRS field who want to perform
  • researchers who want to access to large amount of high quality neuroimaging datasets for training and testing
  • biophotonics researcher who want to share their optical (NIRS, DOT, photoacoustic, microscopy data etc)
  • Preprocessing, GLM, optode co-registration, image reconstruction.
  • Creating custom script-based analysis pipelines. 

Course Plan

Level: Introductory

Pre-Requisites: Users must have a Google account and Google Drive; all training materials will be done via Jupyter Notebook in a web browser, running via the free virtual machines provided by Google Colab.
Course Duration: 2 hours

Delivery Plan

– A hands-on introduction to NeuroJSON.io website
– Tutorial on how to query and download NeuroJSON.io datasets on the command line
– Dynamically query and download NeuroJSON.io datasets in MATLAB
– Dynamically access NeuroJSON.io datasets in Python
– A hands-on demo to the NoSQL database backend

Why enrol on this course?

NeuroJSON.io is a US NIH-funded project aiming at developing a comprehensive, searchable, and reusable neuroimaging data-sharing platform. Built upon JSON and NoSQL database technologies, NeuroJSON.io is highly scalable and has currently hosted over 1,000 BIDS (brain imaging data standard) compatible datasets, including multimodal measurement data for over 40,000 subjects. It also supports diverse data types, including various brain atlases, fNIRS SNIRF data, brain mesh models, among others. NeuroJSON.io platform also implements sophisticated metadata extraction mechanisms, making every dataset searchable and easily reusable.

A unique feature in NeuroJSON.io is that every dataset can be accessed via a URL-based REST API, making it possible to process large amounts of neuroimaging data resources for large-scale data analysis, machine learning training, and meta-analyses conveniently in nearly all programming language environments such as MATLAB, GNU Octave and Python.