Reconstruct Liver in Tomviz

Overview

Approximate time: 3hrs (~2.5 to reconstruct)

Download Liver Data

Convert to tif

Import to tomviz

Form and Execute Pipeline:

set tilt angles

image align

adjust rotation center angle 

adjust rotation center position

reconstruct

Download Liver Data

The dataset for this tutorial is an x-ray tilt series of a liver. Download liver.avi from Google Drive. 

The file you downloaded can be viewed in Google Drive or with VLC.

Convert to .tif

Tomviz can't take an avi file as input so we must convert it to a multipage tif file. This can be done in two steps, using two different command line tools, first to decompose the video into frames, then to package them into a tif. 

Install ffmpeg and imagemagick.

Once downloaded and installed, open terminal and navigate to the same directory as liver.avi

Decompose the video:

ffmpeg -i liver.avi frame_%03d.png

The %03d tells ffmpeg that the ordinal number of each output image will be formatted using 3 digits.

Make the tif:

convert *.png liver.tif

Now we have the liver in a format compatible with tomviz!

Import to tomviz

Open tomviz. 

In the toolbar on top click: file > open data

Select the newly created liver.tif and click open.

Form and Execute Pipeline

Before we reconstruct, there are some configurations we must do to increase the accuracy of the reconstruction.

1. Informs the program that our input is a tilt series (as opposed to a stack of sinograms)

   • Tomography > Mark Data As Tilt Series

2. The liver may have moved while scanning, so realign the images to account for object movement. 

   • Tomography > Image Alignment (Auto: Cross Correlation)

3. The default setting is not the appropriate rotation axis, so first align it so its the right angle

   • Tomography > Tilt Axis Rotation Alignment (Auto)

4. Shift it so its properly centered 

   • Tomography > Tilt Axis Shift Alignment (Auto)

5. Finally, this last one take a while. Perform the reconstruction. There are plenty of options but a good option that balances accuracy and efficiency is weighted back projection. Just run it with all the default settings.

   • Tomography > Weighted Back Projection