Multienergy Fan Beam Computed Tomography Dataset of a Bird Chest Imaged with 3 Different X-ray Spectra

Summary

This dataset is a collection of X-ray projection data of a biological imaging phantom (a bird chest) imaged in an X-ray microtomography scanner, using three different X-ray spectra. The dataset also includes a metadata file for each of the scans, specifying the scan geometry and other important scan parameters, as well as photographs and example reconstructions. The dataset is designed for use in algorithm development for multienergy computed tomography.

Description

Sample Information

The sample is the chest of a common quail (Coturnix coturnix) bird obtained frozen from a local supermarket. The chest section of the frozen bird was removed using a handsaw, and left to melt and settle in a sample holder before imaging.

Scanner

The measurement data were acquired using an X-ray microtomography scanner in the University of Helsinki Micro-CT Laboratory. The scanner uses cone beam geometry and it is equipped with an end-window tube with a tungsten target.

Scan Settings

The dataset consists of three consecutive scans made using identical geometry but different X-ray spectra and detector exposure times. For each scan, 720 X-ray projections were acquired using an angle increment of 0.5 degrees. Multiple frames were averaged for each projection in order to increase signal-to-noise ratio. The scan geometry and the energy-specific settings are summarized in the following two tables.

Table 1. Imaging geometry used for collecting the data.

Table 2. Energy-specific settings used for collecting the data.

Data Post-Processing

Before the scans were made, a dark current image and flat-field image were acquired for each scan setting. During the scans, dark current subtraction and flat-field correction were automatically applied to the X-ray projections by the measurement software.

Data Contents

This dataset contains the following files:

• The raw projection data (.tif format) for each scan and a metadata file (.txt format) describing the measurement setup, with formatting that is both human-readable and machine-readable.
• Pre-created 2D sinograms for each energy level. The sinograms have been created from the central plane of the cone beam, which reduces to fan beam geometry. The sinograms are stored in Matlab's .mat file format in data structures which also contain metadata on the measurement.
• Photographs taken during the measurement process.
• Example filtered backprojection (FBP) reconstructions of the central plane of the phantom for each energy. The reconstructions were computed using the  Phoenix datos|x CT software provided with the microtomography scanner

Research Group

This dataset was produced by the Inverse Problems research group at the Department of Mathematics and Statistics at the University of Helsinki, Finland (https://www.helsinki.fi/en/researchgroups/inverse-problems) in collaboration with the Computational Physics and Inverse Problems research group at the University of Eastern Finland, Finland (https://sites.uef.fi/inverse) and the X-ray Laboratory at the Department of Physics at the University of Helsinki, Finland (https://www.helsinki.fi/en/researchgroups/x-ray-laboratory).

Previous Use

This dataset has been used in the following publications:

Jussi Toivanen, Alexander Meaney, Samuli Siltanen, Ville Kolehmainen. Joint reconstruction in low dose multi-energy CT. Inverse Problems and Imaging, 2020, 14(4): 607-629. doi: 10.3934/ipi.2020028.

E. Cueva, A. Meaney, S. Siltanen, M. J. Ehrhardt. Synergistic multi-spectral CT reconstruction with directional total variation. Philos Trans A Math Phys Eng Sci. 2021 Aug 23;379(2204):20200198. doi: 10.1098/rsta.2020.0198.

Additional Links

To get started with the data, we recommend looking at the HelTomo toolbox, specifically created for working with CBCT data collected by the Inverse Problems research group, and available at https://se.mathworks.com/matlabcentral/fileexchange/74417-heltomo-helsinki-tomography-toolbox.

Acknowledgements

We wish to thank laboratory engineer Heikki Suhonen for his guidance and assistance in conducting the measurements.

Contact Details

For more information or guidance in using these datasets, please contact alexander.meaney [at] helsinki.fi.