Reconstruct Liver in Tomviz
Zachary Mor
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.
Informs the program that our input is a tilt series (as opposed to a stack of sinograms)
Tomography > Mark Data As Tilt Series
The liver may have moved while scanning, so realign the images to account for object movement.
Tomography > Image Alignment (Auto: Cross Correlation)
The default setting is not the appropriate rotation axis, so first align it so its the right angle
Tomography > Tilt Axis Rotation Alignment (Auto)
Shift it so its properly centered
Tomography > Tilt Axis Shift Alignment (Auto)
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