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
- Sample preparation and parameters: Samples are prepared, mounted and positioned; X-ray source parameters and detector parameters are set
- 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)
- 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
- Post Processing, such as Segmentation, Quantification, Statistics
- Data Curation, including Metadata Preparation and Repository ingest of the data
Involved Disciplines
Civil Engineering, Mechanics, Physics, Mathematics
Data Streams
- The primary research / raw data after the XRCT scan (this output serves as input for the subsequent step, or other research endeavours)
- 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 , $y$, ($z$), .., 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
Reproducibility of the Experiments on the original Devices/Instruments/Hardware
Reproducibility of the Experiments on other Devices/Instruments/Hardware
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/