iTCGA: Visualization and Medical Imaging

https://blogs.umb.edu/elevate/

BIWOC Research Hub

Research Experience for Undergraduate Students in CS and Engineering

2023 Students

2024 Students

The Mini-PhD!

accepted papers

grad school applications

https://STEMPOWER.net

Daniel Haehn

MACHINE

PSYCHOLOGY

DANIELHAEHN.COM

Scientific Visualization

https://dataverse.harvard.edu/dataverse/omama

2D Cancer Annotation

https://slicedrop.com

3D Visualization for Surgical Planning

Kourosh's Gene Expression Data

Information Visualization

Data Visualization

https://visualizing.boston

https://nishikalewis.github.io/Visualizing-Massachusetts/Women_owned_Businesses/index.html

https://wilhenalbertohm.github.io/Labor-Migration-Vis/view/

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!

https://thoughtbot.com/blog/analyzing-minards-visualization-of-napoleons-1812-march

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?

https://colorbrewer2.org

Let's make a chart beautiful!

What's wrong with this chart?

Source: World Bank

bit.ly/uglyvis

Choose 1 example of a bad visualization and
tell us what is wrong about it and how to improve it!

Scientific Visualization

Brain Camera

MRI Scanner

CT Scanner

Fetal MRI

Image Volumes

Marching Cubes creates 3D Meshes

Bill Lorensen 1987

Label Maps

R.I.P.

https://haehn.github.io/blum/

https://haehn.github.io/blum/hd.html

Coronal

Super-Resolution

Coronal

Super-Resolution

Image Volumes

Meshes

DTI Fibers

Radiology

0.1 - 1 mm^3 voxel size

< 1 Gigabyte

https://slicedrop.com/reloaded/

MeshAR

FibersAR

GPU Access!

the most popular one!

XTK: the easiest!

brandnew + fast

https://portal.imaging.datacommons.cancer.gov/

https://cs666.org/data/tumor

<html>
<head>
  <style>

    body {
      background: black;
      margin: 0;
      padding: 0;
      overflow: hidden !important;
    }
    
  </style>

  <script type="text/javascript" src="https://get.goXTK.com/xtk_edge.js"></script>
  <script>

  window.onload = function() {

    r = new X.renderer3D();
    r.init();
        
    tumor = new X.mesh();
    tumor.file = 'tumor.vtk';
        
    r.add(tumor);
        

    tracks = new X.fibers();
    tracks.file = 'tracks.trk';
        
    r.add(tracks);
        

    volume = new X.volume();
    volume.file = 'volume.nii';
        
    r.add(volume);

    r.render();


  }
  </script>
</head>

<body>
</body>
</html>

MRI

Electron Microscope

millimeter resolution

nanometer resolution

Connectomics

Brain Connectivity at Synapse Level

nanometer resolution!

tera- or petabytes of data!

Drosophila Hemibrain Connectome

8x8x8nm^3 voxel size

~25,000 neurons

https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/base.json

Google + Janelia

X-ray Crystallography

MRI

Electron Microscope

one ten-billionth (10^-10) of a meter

Why is it called "guardian of the genome"?

p53 helps prevent cancer development by inhibiting growth and division of cells which damage DNA.

mutations in p53 are found in approximately half of all cancers!

Tumor Suppressor

Cho Y, Gorina S, Jeffrey PD, Pavletich NP. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science. 1994 Jul 15;265(5170):346-55.