Follow along at: https://arokem.github.io/2019-OHBM-AFQ-Browser

A browser-based tool for visualization and analysis of diffusion MRI data

Jason Yeatman
(UW ILABS)

Adam Richie-Halford
(UW eScience)

Josh Smith
(UW eScience)

Anisha Keshavan
(UW eScience →
Child Mind Institute)

Ariel Rokem
(UW eScience)

Normal behavior is supported by brain networks

Studying brain networks

Not just static cables!

Brain connections develop and mature with age

Individual differences account for differences in behaviour

Adapt and change with learning

Diffusion MRI measures the physical properties of brain connections

Diffusion MRI

Diffusion MRI

Diffusion MRI

Diffusion MRI

Diffusion statistics

Mean diffusivity

Fractional anisotropy

Principal diffusion direction

The 3D structure of each brain is unique

Tracts provide the anatomically correct coordinate frame

The 3D structure of each brain is unique

Tracts provide the anatomically correct coordinate frame

Automated Fiber Quantification (Tractometry)

Amyotrophic Lateral Sclerosis (ALS)

Yeatman et al. (2012)
Sarica et al. (2017)

Challenges:

Results from large multi-dimensional datasets are hard to understand

Hard to communicate

Hard to reproduce

Data sharing is not incentivized and is not easy enough

Solution: a tool for exploratory data analysis with data sharing built in!

Exploratory data analysis

Linking and brushing

Exploratory data analysis

Enhances published results

Linked visualizations facilitate easy exploration

Enables new discoveries in old datasets

A browser-based tool for visualization and analysis of diffusion MRI data

A web-based application

Leverages modern visualization frameworks

Builds a web-site for a diffusion MRI dataset

Automatically uploads the website to GitHub

https://yeatmanlab.github.io/Sarica_2017

Exploratory data analysis

Enhances published results

Linked visualizations facilitate easy exploration

Enables new discoveries in old datasets

Example

Automatic data sharing

http://afqvault.org

Further exploration

Data sharing facilitates interdisciplinary collaboration

Dimensionality reduced data in tidy table format

Facilitates interdisciplinary collaboration

Install

pip install afqbrowser

CLI

Code

Thanks!