Analysis and Visualization of Life Sciences Data



Teodora Szasz

Image Analysis & Data Visualization Specialist

tszasz@uchicago.edu

Thursday, May 23, 2018

Research Computing Center

Imagining the Inner Life of a Cell


While red blood cells are carried away at high velocity by a strong blood flow, leukocytes roll slowely on endothelial cells...

Visualizing the Inner Life of a Cell


Visualizing villi cells inside human intestine

Department of Surgery, UChicago


							1.5007,5.0234,-2,0
							0.50861,5.005,-3,0
							-0.093727,1.5029,-8,0
							2.5,-0.15178,-10,0
							5.1054,1.5033,-9,0
							-0.010013,4.4828,-6,0
							4.4713,-0.016689,-10,0
							1.5022,5.0703,-6,0
							-0.082011,3.4974,-7,0
							4.4484,5.03,-18,0
							0.50287,5.0017,-1,0
							-0.0033378,4.4943,-2,0
							-0.035148,3.4989,-3,0
							-0.060711,2.5,-4,0
							-0.058579,1.5018,-5,0
							4.4971,-0.0016689,-1,0
							-0.011716,1.5004,-1,0
							3.4996,5.0117,-1,0
							3.4974,5.082,-7,0
							..................
						

OSPRay - a ray tracing based rendering engine for high-fidelity visualization

From visualizing human cells to visualizing cephalopod cells...

Octopus camouflage

Characterizing the reflectivity in cephalopod skin: a challenge for 3D segmentation

Marine Biology Laboratory, UChicago

Tools used: Fiji, ITK, Matlab(Image Processing Toolbox)

Segmentation of iridocytes using Frangi method

Segmentation of leucocytes using 3D Watershed method

Segmentation of other unusual shapes

From cells to neurons...

Reconstructing neuronal lineages using whole-brain cell tracking on Midway supercomputer

Department of Organismal Biology and Anatomy, UChicago

Tools used: Imaris, ITK, Matlab(Image Processing Toolbox)

3D rendered data and neurons tracking information

From neurons to human organs...

Developing Image Analysis and Visualization Tools for Improving Prostate Cancer Diagnosis using MRI images

Department of Radiology, UChicago

Tools used: 3D Slicer, ITK

Web based tool for displaying and registering mp-MRI data sets with histopathology images

3D Non-Rigid Registration between MRI and Histopathology

From humans to machines...

Artificial Intelligence in Life Sciences...

Artificial Neural Networks in Radiology

New to deep learning in radiology?

Deep Learning in Radiology: Recent Advances, Challenges, and Future Trends

Virtual Reality in Life Sciences...

Explortory Visualization: 4D Heart Blood Flow Data in VR

BentoBox was developed in collaboration with the University of Minnesota’s Interactive Visualization Lab

RCC's past and future workshops available to download

https://rcc.uchicago.edu/support-and-services/workshops-and-training

Join the Visualization Team on Slack

  • Join the RCC's image analysis and visualization Slack team