TomViz Tutorial

By Shreya D'Souza

AN INTRODUCTION TO TOMVIZ

The Tomviz application is used to visualize electron tomography data, that is data that "attempts to reconstruct 3D objects from 2D projection images taken at different viewing angles, or tilts—producing the entire internal structure of a specimen or region of interest.". It typically involves viewing nanoscale materials under a scanning transmission electron microscope.

Method of obtaining data

Focused electron beam with sub-nanometer diameter is rastered across sample of interest
Electrons scattered from sample recorded by annular dark field detector
- Generates 2D projection image of sample
Viewing angle is changed by rotating the specimen
Images are aligned to obtain a common axis of rotation

This type of data lends itself for visualisation in virtual reality, so I thought it would be a good software to explore! The goal of this tutorial is to show you another way in which scientific data can be visualised and demonstrate the intersection between Virtual Reality and scientific data.

This tutorial uses very few of the many ways TomViz can be used, so it is a good introduction but definitely does not explore all the different capabilities of TomViz! This tutorial is more focused on getting the data to Paraview so that it can be ported to the YURT, so it makes use of the sample data available in TomViz. Ultimately, TomViz is an incredibly useful tool with many analytical tools not explored in this tutorial, and those interested in scientific research can find many additional sources of data online. However, a more in-depth explanation of how to interact with data in Tomviz, as well as data sources, can be found here: https://www.cambridge.org/core/journals/microscopy-today/article/tutorial-on-the-visualization-of-volumetric-data-using-tomviz/55B58F40A16E96CDEB644202D9FD08BB/core-reader.

SETTING UP

Download TomViz here: https://tomviz.org/downloads/
Download Paraview here: https://www.paraview.org/download/

OPENING A SAMPLE DATASET

Upon opening TomViz, select the option to view the sample data. This should open a volume of a reconstructed nanoparticle.

MANIPULATING THE DATA

Not part of the tutorial, but some ways in which the data can be manipulated to produce various visualizations!

Changing the colours represented

colour.mov

EXPORTING A VOLUME

The left side of the screen should have a pipelines toolbar. Left-click on the volume and select "Export As Volume"
Choose the option to export as a .pvd file.
Open Paraview
Navigate to the file in File > Open. You should now see an outline on your screen.
In order to see the volume, double-click on the volume the pipeline folder to open Properties
Select Volume as the Representation. This will display the volume, as shown below.

Volume.mov

PORTING TO THE YURT

Follow Spencer's tutorial here!

SOURCES

https://www.nature.com/articles/sdata201641

https://tomviz.org/

https://www.cambridge.org/core/journals/microscopy-today/article/tutorial-on-the-visualization-of-volumetric-data-using-tomviz/55B58F40A16E96CDEB644202D9FD08BB/core-reader

https://tomviz.org/wp-content/uploads/2017/03/TomvizBasicUserGuide.pdf