XRCT

XRCT Datasets as experimental research data

This use case is kindly provided by Prof. Holger Steeb and Matthias Ruf (MIB/University of Stuttgart).

PID:

• Publication: 10.1063/5.0019541
• Related dataset: 10.18419/darus-639

Problem Statement

Porous media, specifically open-pored asphalt concrete, is analysed with an (µ)XRCT (micro X-ray Computed Tomography) scanner. The scanner is a modular hardware system to implement advanced in situ setups

Object of Research and Objective

Porous media analysis, e.g. to detect micro fractures or investigate fatigue behaviour.

Procedure

The whole process of XRCT Scan

1. Sample preparation and parameters: Samples are prepared, mounted and positioned; X-ray source parameters and detector parameters are set
2. XRCT Scan: Recording of the primary / raw data (in this specific case the "radiograms") (in two phases: open beam (flat field) and dark images (dark field) (before the actual scan) and object projection image (the actual scan)

A radiogram, the output of step 2

3. 

   A tomogram, output of the image reconstructions in step 3

   Image Processing/Reconstruction, that generates the research data (in this specific case "tomograms") from the primary/raw data. Core parts are the reconstruction algorithm, filters, linearization and normalization and correction methods

4. Post Processing, such as Segmentation, Quantification, Statistics
5. Data Curation, including Metadata Preparation and Repository ingest of the data

Involved Disciplines

Civil Engineering, Mechanics, Physics, Mathematics

Data Streams

1. The primary research / raw data after the XRCT scan (this output serves as input for the subsequent step, or other research endeavours)
2. The research data generated by reconstruction algorithms, filters, linearization, normalization and correction methods from the primary/raw data.

Model

Discretization

• Time: -
• Space 2D Voxel size $x$, $y$, ($z$), .., ROI off-size $x$, $y$, ($z$); Position $x$, $y$, ($z$)

Variables

Name	Unit	Symbol	dependent (measured) / independent (controlled)

Parameter

Name	Unit	Symbol

Process Informationen

Process Steps

Name	Description	Input	Output	Method	Parameter	Environment	Mathematical Area
Sample preparation and parameters	a. Samples are prepared, mounted and positioned b. X-ray source parameters and detector parameters are set		X-Ray and Detector parameters	Pre-Filters
XRCT Scan to generate the primary / raw data (in this specific case the "radiograms")	Recording of the data in two phases: a. open beam (flat field) and dark images (dark field) (before the actual scan) b. object projection image (the actual scan)	Sample; X-Ray and Detector parameters; Geometric Information	Projections, flat field images, dark field images	XRCT Scan	X-ray source parameters (tube voltage, tube flux, phys. pre-filters), detector parameters (binning mode, exposure time, number of image per projection, number of projection angles)
Image Processing/Reconstruction to generate research data (in this specific case "tomograms")	Image Processing/Reconstruction in following steps: a. Normalization and Linearization of the projection images -> Transforming the data into sinograms b. Correction of geometrical system misalignments c. Filters d. Reconstruction Algorithm e. Evaluation of the reconstructed data set	X-Ray and Detector parameters; Projections, flat field images, dark field images	Reconstructions	Normalization, Linearization, Filters (Spot, Ring, Noise), Reconstruction Algorithms (FBP, SIRT, SART)	Source-Detector-Distance, Source-Object-Distance
Post Processing	Additional steps, such as segmentation, quantification, statistics	Reconstructions	Reconstructions	Segmentation
Data Curation	Step to make the data openly availably in a repository	Projections, Reconstructions, Metadata	10.18419/darus-639

Applied Methods

ID	Name	Process Step	Parameter	realised/implemented by
wikidata:Q20665529	Filtered Back Projection (FBP)	Image Processing/Reconstruction		Octopus Reconstruction
	Simultaneous iterations reconstruction technique (SIRT)	Image Processing/Reconstruction
wikidata:Q22908794	Simultaneous algebraic reconstruction technique (SART)	Image Processing/Reconstruction
	Ring Filter	Pre-Processing, Image Processing/Reconstruction, Post Processing
	Spot Filter	Pre-Processing, Image Processing/Reconstruction, Post Processing
	Noise Filter	Pre-Processing, Image Processing/Reconstruction, Post Processing
wikidata:Q17104971	Normalization	Image Processing/Reconstruction
wikidata:Q1520713 (?)	Linearization	Image Processing/Reconstruction
wikidata:Q56933	Segmentation	Post Processing

Software used

ID	Name	Description	Version	Programming Language	Dependencies	versioned	published	documented
	Xilab	Motion controller for the scans	1.14.12		Windows,Linux	closed source		yes (https://files.xisupport.com/Software.en.html)
wikidata:Q169478, sw:558	MATLAB	(Scan Controlling) Controlling the scan loop; Interaction with HW implmented by socket programmiing		C, C++, Fortran, Java		closed source; proprietary		yes (https://de.mathworks.com/help/)
sw:29944	Octopus Reconstruction	(Reconstruction) Software performing the tomographic reconstruction based on the projection images as well as beam profile and dark images; Remark: Software was discontinued 2019	Version 8.9.4-64 bit					not any more
sw:14524	Astra Toolbox	(Reconstruction) Software performing the tomographic reconstruction based on the projection images as well as beam profile and dark images, but next to analytical also algebraic reconstruction methods			Matlab, Python	yes	yes (https://github.com/astra-toolbox/astra-toolbox)	yes
wikidata:Q5425748, sw:9754	Fiji	(Image Processing) Evaluation of the captured images; Fiji is a distribution of ImageJ		Shell, Java, Matlab, Python		yes	yes (https://github.com/fiji/fiji)	yes
wikidata:Q4829059, sw:18539	Avizo	(Image Processing) Evaluation of the captured images, such as segmentation				no	no, proprietary	yes (https://www.thermofisher.com/de/de/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html)

(There are also mentioned but not yet tested software packages as alternatives in the paper )

Experimental Devices/Instruments and Computer-Hardware

ID	Name	Description	Version	Part Nr	Serial Nr	Location	Software
	Dexla 1512 Detektor

Input Data

ID	Name	Size	Data Structure	Format Representation	Format Exchange	binary/text	proprietary	to publish	to archive

Output Data

ID	Name	Size	Data Structure	Format Representation	Format Exchange	binary/text	proprietary	to publish	to archive
	XRCT scan raw data	$O(GB)$	-	tiff	-	image	?	?	yes
doi:10.18419/darus-639	micro-XRCT data set of open-pored asphalt concrete; projections and reconstruction	$O(GB)$	-	tiff	rar	image	open	yes	yes

Reproducibility

Transferability of the Experiments to

a) similar model parameters

b) other models

Legend

The following abbreviations are used in the document to indicate/resolve IDs:

doi: DOI / https://dx.doi.org/

sw: swMATH / https://swmath.org/software/

wikidata: https://www.wikidata.org/wiki/