iTCGA: Visualization and Medical Imaging

Daniel Haehn

Scientific Visualization

2D Cancer Annotation

3D Visualization for Surgical Planning

Kourosh's Gene Expression Data

Information Visualization

Data Visualization

Scientific Visualization == black background

Information Visualization == white background

Charts

as building blocks

Information Visualization

Data Visualization

Who has the most #1s?

Who has the least?

Tables are visualizations too!

this is one is better

Visualizations should reduce the cognitive load when looking at data!

Bad Examples

Information Visualization

Line Chart Aspect Ratio

Pie Charts

3D plots can lead to occlusion and confusion

and these are ugly colors!!

Colors!

Can you tell which color represents higher or lower values?

Let's make a chart beautiful!

What's wrong with this chart?

Source: World Bank

Scientific Visualization

BYOD!

Brain Camera

MRI Scanner

CT Scanner

Fetal MRI

Image Volumes

2D

3D

Marching Cubes creates 3D Meshes

Bill Lorensen 1987

Label Maps

R.I.P.

Ron Kikinis

B. Leonard Holman Professor of Radiology, Harvard Medical School

Download the same data to 3D Slicer using the IDC Browser extension!

Then, we will do Volume Rendering to analyze data and create a segmentation mesh of the tumor.

After export, let's load it in SliceDrop!

or BYOD!

window.onload = function() {

    r = new X.renderer3D();
    r.init();
    
    volume = new X.volume();
	volume.file = 'https://fly.cs.umb.edu/data/X/daniel.nii';
    
    r.add(volume);
    
    r.render();
    
}

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Visualization and Medical Imaging @iTCGA

By Daniel Haehn

Visualization and Medical Imaging @iTCGA

Research Immersion in Cancer Genomics: Genomics & Data Science Workshop

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