XRCT: Difference between revisions

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=== Procedure ===
=== Procedure ===
[[File:XRCT process.png|thumb|The whole process of XRCT Scan]]


[[File:https://i.imgur.com/YwPesH7.png]]


# Sample preparation and parameters: Samples are prepared, mounted and positioned; X-ray source parameters and detector parameters are set
# 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)
# 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)


![]([https://i.imgur.com/H4QDBOD.png https://i.imgur.com/H4QDBOD.png] =250x250)
[[File:XRCT radiogram.png|thumb|A radiogram, the output of step 2 ]]


<ol start="3">
<ol start="3">
<li>Image Processing/Reconstruction, that generates the research data (in this specific case &quot;tomograms&quot;) from the primary/raw data. Core parts are the reconstruction algorithm, filters, linearization and normalization and correction methods</li></ol>
<li>[[File:XRCT tomogram.png|thumb|A tomogram, output of the image reconstructions in step 3]]Image Processing/Reconstruction, that generates the research data (in this specific case &quot;tomograms&quot;) from the primary/raw data. Core parts are the reconstruction algorithm, filters, linearization and normalization and correction methods</li></ol>
 
![]([https://i.imgur.com/8rDvQHJ.png https://i.imgur.com/8rDvQHJ.png] =250x250)


<ol start="4">
<ol start="4">
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* Time: -
* Time: -
* Space 2D Voxel size $x$, $y$, ($z$), .., ROI off-size $x$, $y$, ($z$); Position $x$, $y$, ($z$)
* Space 2D Voxel size <math>x</math>, <math>y</math>, (<math>z</math>), .., ROI off-size <math>x</math>, <math>y</math>, (<math>z</math>); Position <math>x</math>, <math>y</math>, (<math>z</math>)


=== Variables ===
=== Variables ===


{|
{| class="wikitable"
! Name
! Name
! Unit
! Unit
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=== Parameter ===
=== Parameter ===


{|
{| class="wikitable"
! Name
! Name
! Unit
! Unit
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=== Process Steps ===
=== Process Steps ===


{|
{| class="wikitable"
! Name
! Name
! Description
! Description
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=== Applied Methods ===
=== Applied Methods ===


{|
{| class="wikitable"
! ID
! ID
! Name
! Name
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! realised/implemented by
! realised/implemented by
|-
|-
| wikidata:Q20665529
| wikidata:[[wikidata:Q20665529|Q20665529]]
| Filtered Back Projection (FBP)
| Filtered Back Projection (FBP)
| Image Processing/Reconstruction
| Image Processing/Reconstruction
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|
|
|-
|-
| wikidata:Q22908794
| wikidata:[[wikidata:Q22908794|Q22908794]]
| Simultaneous algebraic reconstruction technique (SART)
| Simultaneous algebraic reconstruction technique (SART)
| Image Processing/Reconstruction
| Image Processing/Reconstruction
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|
|
|-
|-
| wikidata:Q17104971
| wikidata:[[wikidata:Q17104971|Q17104971]]
| Normalization
| Normalization
| Image Processing/Reconstruction
| Image Processing/Reconstruction
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|
|
|-
|-
| wikidata:Q1520713 (?)
| wikidata:[[wikidata:Q1520713|Q1520713]] (?)
| Linearization
| Linearization
| Image Processing/Reconstruction
| Image Processing/Reconstruction
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|
|
|-
|-
| wikidata:Q56933
| wikidata:[[wikidata:Q56933|Q56933]]
| Segmentation
| Segmentation
| Post Processing
| Post Processing
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=== Software used ===
=== Software used ===


{|
{| class="wikitable"
! ID
! ID
! Name
! Name
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| yes ([https://files.xisupport.com/Software.en.html https://files.xisupport.com/Software.en.html])
| yes ([https://files.xisupport.com/Software.en.html https://files.xisupport.com/Software.en.html])
|-
|-
| wikidata:Q169478, sw:558
| wikidata:[[wikidata:Q169478|Q169478]], sw:[https://swmath.org/software/558 558]
| MATLAB
| MATLAB
| (Scan Controlling) Controlling the scan loop; Interaction with HW implmented by socket programmiing
| (Scan Controlling) Controlling the scan loop; Interaction with HW implmented by socket programmiing
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| yes ([https://de.mathworks.com/help/ https://de.mathworks.com/help/])
| yes ([https://de.mathworks.com/help/ https://de.mathworks.com/help/])
|-
|-
| sw:29944
| sw:[https://swmath.org/software/29944 29944]
| Octopus Reconstruction
| 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
| (Reconstruction) Software performing the tomographic reconstruction based on the projection images as well as beam profile and dark images; Remark: Software was discontinued 2019
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| not any more
| not any more
|-
|-
| sw:14524
| sw:[https://swmath.org/software/2994414524 14524]
| Astra Toolbox
| 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
| (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
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| yes
| yes
|-
|-
| wikidata:Q5425748, sw:9754
| wikidata:[[wikidata:Q5425748|Q5425748]], sw:[https://swmath.org/software/299449754 9754]
| Fiji
| Fiji
| (Image Processing) Evaluation of the captured images; Fiji is a distribution of ImageJ
| (Image Processing) Evaluation of the captured images; Fiji is a distribution of ImageJ
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| yes
| yes
|-
|-
| wikidata:Q4829059, sw:18539
| wikidata:[[wikidata:Q4829059|Q4829059]], sw:[https://swmath.org/software/2994418539 18539]
| Avizo
| Avizo
| (Image Processing) Evaluation of the captured images, such as segmentation
| (Image Processing) Evaluation of the captured images, such as segmentation
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=== Experimental Devices/Instruments and Computer-Hardware ===
=== Experimental Devices/Instruments and Computer-Hardware ===


{|
{| class="wikitable"
! ID
! ID
! Name
! Name
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=== Input Data ===
=== Input Data ===


{|
{| class="wikitable"
! ID
! ID
! Name
! Name
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=== Output Data ===
=== Output Data ===


{|
{| class="wikitable"
! ID
! ID
! Name
! Name
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|
|
| XRCT scan raw data
| XRCT scan raw data
| $O(GB)$
| <math>O(GB)</math>
| -
| -
| tiff
| tiff
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| doi:10.18419/darus-639
| doi:10.18419/darus-639
| micro-XRCT data set of open-pored asphalt concrete; projections and reconstruction
| micro-XRCT data set of open-pored asphalt concrete; projections and reconstruction
| $O(GB)$
| <math>O(GB)</math>
| -
| -
| tiff
| tiff
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wikidata: [https://www.wikidata.org/wiki/ https://www.wikidata.org/wiki/]
wikidata: [https://www.wikidata.org/wiki/ https://www.wikidata.org/wiki/]
[[Category:Workflow]]

Latest revision as of 17:18, 15 November 2022

XRCT Datasets as experimental research data

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

PID:

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
  1. 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
  1. Post Processing, such as Segmentation, Quantification, Statistics
  2. 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

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 - tiff - image ? ? yes
doi:10.18419/darus-639 micro-XRCT data set of open-pored asphalt concrete; projections and reconstruction - 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/

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