micro-XRCT data sets of subflorescent salt crusts from evaporation of MgSO4 solution with 0.96 mol/L initial concentration

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Ruf, Matthias; Lee, Dongwon; Piotrowski, Joseph; Huisman, Johan Alexander; Steeb, Holger, 2021, "micro-XRCT data sets of subflorescent salt crusts from evaporation of MgSO4 solution with 0.96 mol/L initial concentration", https://doi.org/10.18419/darus-2003, DaRUS, V1

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Subtitle	Reconstructed and segmented data of crusts at 40%, 30%, and 25% saturation in F32 quartz sand
Description	This data set contains data of scans of three separated dry salt crusts that formed by evaporation of magnesium sulfate solution with 0.96 mol/L initial concentration from F32 quartz sand at 40%, 30%, and 25% saturation inside the sand packing. The cylindrical sample holder from polymethyl methacrylat (PMMA) had a diameter of 31 mm and a wall thickness of 5 mm. The crusts consisted of sand grains (F32, Quarzwerke Frechen, mean grain size 240 µm), solid salt (particularly magnesium sulfate tetra hydrate), and air. Other magnesium sulfate hydrates may have precipitated (i.e. magnesium sulfate hepta hydrate, hexa hydrate, mono hydrate). The scanned domain with a diameter of 11.76 mm and a resolution of 4 µm per voxel was located in the radial center of the crust. Details of the scan are listed in the process meta data. The reconstructed data is segmented into four phases, outside, void, salt, and sand (for details see below).
Subject	Chemistry; Computer and Information Science; Earth and Environmental Sciences; Engineering
Keyword	Micro X-Ray Computed Tomography (micro-XRCT), Porous Media, Magnesium Sulfate, Salt Precipitation From Evaporation, Subflorescent Salt Crust Formation
Notes	Ruf, M., Lee, D., and Piotrowski, J. contributed equally.
Data Generation	Experiment
License/Data Use Agreement	CC BY 4.0

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	reconstructed_096_mol-L_025_sat.tar.gz Data_sets_saturation_0.25/Gzip Archive - 14.7 GB Published Sep 9, 2021 14 Downloads MD5: 89ae8540f82c95142cff5f97ade44fb4 Reconstructed micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 25% saturation in 16 bit *.tif file format. 2940x2940x1346 voxels with a uniform voxel size of 4.0 µm. (internal ID: 20200928_01_I01)	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	segmented_096_mol-L_025_sat.tar.gz Data_sets_saturation_0.25/Gzip Archive - 150.5 MB Published Sep 9, 2021 18 Downloads MD5: 2c0860d0eb8b3bb6f20fe92c1f6475a7 Segmented micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 25% saturation in 8 bit *.tif file format. 2940x2940x1346 voxels with a uniform voxel size of 4.0 µm.	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	reconstructed_096_mol-L_030_sat.tar.gz Data_sets_saturation_0.30/Gzip Archive - 11.5 GB Published Sep 9, 2021 12 Downloads MD5: a044d1789df4a737c589047a716fe1b9 Reconstructed micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 30% saturation in 16 bit *.tif file format. 2940x2940x1031 voxels with a uniform voxel size of 4.0 µm. (internal ID: 20200925_01_I08)	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	segmented_096_mol-L_030_sat.tar.gz Data_sets_saturation_0.30/Gzip Archive - 150.5 MB Published Sep 9, 2021 19 Downloads MD5: aad27d428440c86a07f4c6bccbbeeb19 Segmented micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 30% saturation in 8 bit *.tif file format. 2940x2940x1031 voxels with a uniform voxel size of 4.0 µm.	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	reconstructed_096_mol-L_040_sat.tar.gz Data_sets_saturation_0.40/Gzip Archive - 9.7 GB Published Sep 9, 2021 14 Downloads MD5: cafcfa7bdd099c9e06b6f5cfc2cd9a56 Reconstructed micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 40% saturation in 16 bit *.tif file format. 2940x2940x856 voxels with a uniform voxel size of 4.0 µm. (internal ID: 20200924_01_I10)	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	segmented_096_mol-L_040_sat.tar.gz Data_sets_saturation_0.40/Gzip Archive - 194.4 MB Published Sep 9, 2021 19 Downloads MD5: 056d4ba1d4c030e89a4d190b0ce5ed5b Segmented micro-XRCT data set of the crust segment from 0.96 mol/L initial concentration at 40% saturation in 8 bit *.tif file format. 2940x2940x856 voxels with a uniform voxel size of 4.0 µm.	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	mask_file.tif mask_file/TIFF Image - 26.4 KB Published Sep 9, 2021 73 Downloads MD5: ba5c487a2da3ef23ef1d5a15bc0312c1 The mask file was used during "post processing - segmentation step 1".	Preview "mask_file/mask_file.tif" Access File File Access Public Download Options TIFF Image Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/darus-2003
Publication Date	2021-09-09
Title	micro-XRCT data sets of subflorescent salt crusts from evaporation of MgSO4 solution with 0.96 mol/L initial concentration
Subtitle	Reconstructed and segmented data of crusts at 40%, 30%, and 25% saturation in F32 quartz sand
Author	Ruf, Matthias (University of Stuttgart, Institute of Applied Mechanics (CE)) - ORCID: 0000-0003-0299-5921 Lee, Dongwon (University of Stuttgart, Institute of Applied Mechanics (CE) & SC SimTech) - ORCID: 0000-0002-5359-7803 Piotrowski, Joseph (Jülich Research Center) - ORCID: 0000-0002-3769-0573 Huisman, Johan Alexander (Jülich Research Center, University of Stuttgart) - ORCID: 0000-0002-1327-0945 Steeb, Holger (University of Stuttgart, Institute of Applied Mechanics (CE) & SC SimTech) - ORCID: 0000-0001-7602-4920
Point of Contact	Use email button above to contact. Steeb, Holger (University of Stuttgart, Institute of Applied Mechanics (CE) & SC SimTech)
Description	This data set contains data of scans of three separated dry salt crusts that formed by evaporation of magnesium sulfate solution with 0.96 mol/L initial concentration from F32 quartz sand at 40%, 30%, and 25% saturation inside the sand packing. The cylindrical sample holder from polymethyl methacrylat (PMMA) had a diameter of 31 mm and a wall thickness of 5 mm. The crusts consisted of sand grains (F32, Quarzwerke Frechen, mean grain size 240 µm), solid salt (particularly magnesium sulfate tetra hydrate), and air. Other magnesium sulfate hydrates may have precipitated (i.e. magnesium sulfate hepta hydrate, hexa hydrate, mono hydrate). The scanned domain with a diameter of 11.76 mm and a resolution of 4 µm per voxel was located in the radial center of the crust. Details of the scan are listed in the process meta data. The reconstructed data is segmented into four phases, outside, void, salt, and sand (for details see below).
Subject	Chemistry; Computer and Information Science; Earth and Environmental Sciences; Engineering
Keyword	Micro X-Ray Computed Tomography (micro-XRCT) https://www.wikidata.org/wiki/Q3042540 (Wikidata) Porous Media https://www.wikidata.org/wiki/Q3271208 (Wikidata) Magnesium Sulfate https://www.wikidata.org/wiki/Q1821231 (Wikidata) Salt Precipitation From Evaporation Subflorescent Salt Crust Formation
Notes	Ruf, M., Lee, D., and Piotrowski, J. contributed equally.
Language	English
Producer	University of Stuttgart, Institute of Applied Mechanics (CE) - Chair for Continuum-Mechanics https://www.mib.uni-stuttgart.de/en University of Stuttgart - Cluster of Excellence EXC 2075 "SimTech" https://www.simtech.uni-stuttgart.de
Production Date	2020
Production Location	University of Stuttgart, Institute of Applied Mechanics (CE), Stuttgart, 70569, Germany
Contributor	Rights Holder : Steeb, Holger
Funding Information	DFG: 327154368
Project	SFB 1313 - C05
Data Type	Image data
Related Dataset	Piotrowski, J., Huisman, J. A., (2021). Sample Properties, Evaporation Data, and Pressure Measurements of MgSO4 Crusts on F32 Quartz Sand From 0.96 mol/L, 0.64 mol/L, and 0.32 mol/L Initial Concentration. DaRUS. https://doi.org/10.18419/darus-1861; Ruf, M., Lee, D., Piotrowski, J., Huisman, J.A., Steeb, H., (2021). micro-XRCT data sets of subflorescent salt crusts from evaporation of MgSO4 solution with 0.64 mol/L initial concentration. DaRUS. https://doi.org/10.18419/darus-1848; Ruf, M., Lee, D., Piotrowski, J., Huisman, J.A., Steeb, H., (2021). micro-XRCT data sets of subflorescent salt crusts from evaporation of MgSO4 solution with 0.32 mol/L initial concentration. DaRUS. https://doi.org/10.18419/darus-2002
Other Reference	Ruf, M., & Steeb, H., (2020). An open, modular, and flexible micro X-ray computed tomography system for research. Review of Scientific Instruments, 91(11), 113102. https://doi.org/10.1063/5.0019541

Process Metadata

Processing Methods	micro-XRCT scan of the centered sample (The micro-XRCT data sets were acquired using a cone beam micro-XRCT setup.) ; Parameters: All method parameters with label "1". denoising (The reconstructed data was denoised using adaptive manifold non-local mean (AMNLM) filter in AVIZO Fire.) ; Parameters: AMNLM - Mode, AMNLM - Interpretation, AMNLM - Spatial Standard Deviation, AMNLM - Intensity Standard Deviation, AMNLM - Search Window, AMNLM - Local Neighborhood, AMNLM - CUDA Device segmentation step 1 (The first step of segmentation was performed using the functions "imadjust", "imquantize", "multithresh", and "activecontour" in MATLAB on every slice of each stack. All input parameters that are not explicitly mentioned were default parameters from MATLAB. The mask "mask_file.tif" was applied to every slice of each stack.) ; Parameters: multithresh - threshold, imquantize - levels, activecontour - mask, activecontour - method, activecontour - SmoothFactor segmentation step 2 (The second step of segmentation was performed using the function "kmeans" in MATLAB on every slice of each stack, which was obtained from segmentation step 1. All input parameters that are not explicitly mentioned were default parameters from MATLAB.) ; Parameters: kmeans - clusters, kmeans - Distance
Method Parameters	Geometric magnification "1" [-] : 12.37495 Source detector distance "1" [mm] : 1011.11139 Source object distance "1" [mm] : 81.70633 X-ray tube voltage "1" [kV] : 130 X-ray tube current "1" [µA] : 130 X-ray spectrum filter "1" : no Number of vertical detector pixel "1" [pixel] : 2940 Number of horizontal detector pixel "1" [pixel] : 2304 Detector pixel size "1" [mm] : 0.04950 Resulting voxel size "1" [mm] : 0.0040 Detector exposure time "1" [ms] : 1500 Number of projection angles "1" : 1800 Number of projections per angle "1" : 1 Detector bad pixel map version "1" : "ShadoBox6KHS_v2020-09-03" Detector in-plane (YZ-plane) moving pattern in pixel "1" : [(0,0),(35,35),(35,-35),(-35,35),(-35,-35)] Detector in-plane (YZ-plane) positions "1" : 5 Number of dark images "1" (di) : 1 Number of open beam images "1" (ob) : 1 Position X-axis "1" [mm] : 268.12197 Position Y-axis "1" [mm] : 12.14425 Position Z-axis "1" [mm] : 28.20000 Position x-axis "1" [mm] : -0.14758 Position y-axis "1" [mm] : 0.08000 Position switch detector axis "1" [mm] : 450.00000 Position detector X-axis "1" [mm] : 205.00000 Position detector Y-axis "1" [counts] : 298960 Position detector Z-axis "1" [counts] : 314300 AMNLM - Mode [-] : GPU Adaptive Manifold AMNLM - Interpretation [-] : 3D AMNLM - Spatial Standard Deviation [-] : 5 AMNLM - Intensity Standard Deviation [-] : 0.2 AMNLM - Search Window [px] : 10 AMNLM - Local Neighborhood [px] : 3 AMNLM - CUDA Device [MB] : 3072 : GeForce GTX 780 multithresh - threshold [-] : 3 imquantize - levels [-] : output multithresh activecontour - mask [-] : output imquantize (salt and sand phase only) activecontour - method [-] : Chan-Vese activecontour - SmoothFactor [-] : 1.1 kmeans - clusters [-] : 3 kmeans - Distance [-] : cityblock
Software	Octopus Reconstruction Version: 8.9.4.9 (Vlassenbroeck, J., Dierick, M., Masschaele, B., Cnudde, V., Van Hoorebeke, L., & Jacobs, P. (2007). Software tools for quantification of X-ray microtomography at the UGCT. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 580(1), 442-445. https://doi.org/10.1016/j.nima.2007.05.073) AVIZO Fire Version: 2019.1 (https://www.thermofisher.com/de/de/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html) Academic License (Thermo Fisher Scientific Inc.) MATLAB Version: 2019b (https://de.mathworks.com/products/matlab.html) Academic License (MATLAB. (2019). 9.7.0.1301707 (R2019b). Natick, Massachusetts: The MathWorks Inc.) Image Processing Toolbox Version: 2019b (https://www.mathworks.com/products/image.html) Academic License (Image Processing Toolbox for MATLAB. (2019). Natick, Massachusetts: The MathWorks, Inc.) Statistics and Machine Learning Toolbox Version: 2019b (https://www.mathworks.com/products/statistics.html) Academic License (Statistics and Machine Learning Toolbox for MATLAB. (2019). Natick, Massachusetts: The MathWorks, Inc.)
Instruments	micro-XRCT system (Ruf, M., & Steeb, H. (2020). An open, modular, and flexible micro X-ray computed tomography system for research. Review of Scientific Instruments, 91(11), 113102. https://doi.org/10.1063/5.0019541) , Version: Calibration: "v2020-09-01" X-ray source , Version: FineTec FORE 180.01C TT Detector , Version: Shad-o-Box 6K HS with CsI scintillator Stage X-Axis , Version: Owis LIMES 170-1000-3HSM Stage Y-Axis , Version: Standa 8MT167-25LS-MEn1 Stage Z-axis , Version: Owis HVM-100-30-HSM-MS Stage x-axis , Version: Newport M423 stage with Nanotec ST2018L0804-A stepper motor Stage y-axis , Version: Newport M423 stage with Nanotec ST2018L0804-A stepper motor Stage rotZ-axis , Version: Standa 8MR190-2-28-MEn1 Stage switch detector , Version: ISEL 2111325086/213503 spindle (pitch 2.5 mm) with Vexta PK245M-01B stepper motor Stage detector X-axis , Version: Custom-made: Spindle with 5 mm pitch and Vexta PK245M-01B stepper motor Stage detector Y-axis , Version: Standa 8MTF-75XX-MEn1 Stage detector Z-axis , Version: Standa 8MTF-75XX-MEn1 Multi-axis controller (8 channel) , Version: Standa 8SMC4-ETHERNET Multi-axis controller (12 channel) , Version: Standa 8SMC5-ETHERNET Sample holder (Inner diameter 31 mm, wall thickness 5 mm) , Version: M-BK-2A with custom-made PMMA tube
Processing Steps	1. Generation ; Methods: micro-XRCT scan of the centered sample ; Software: Octopus Reconstruction ; Instruments: all instruments mentioned above ; Output: "reconstructed_096_mol-L"-files 2. Postprocessing ; Methods: denoising, segmentation ; Software: AVIZO Fire, MATLAB ; Input: "reconstructed_096_mol-L"-files, mask_file.tif ; Output: "segmented_096_mol-L*"-files

Engineering Metadata

Data Generation	Experiment
Measured Variables	Void fraction of entire stacks (range) [-] : 0.16 : 0.33 Salt fraction of entire stacks (range) [-] : 0.34 : 0.46 Sand fraction of entire stacks (range) [-] : 0.31 : 0.50
System Phases	F32 quartz sand (Components: > 99.7 w% silicon dioxide) magnesium sulfate (Components: magnesium sulfate) air (Components: oxygen, nitrogen at 20°C and 1 bar)
System or Phase Components	magnesium sulfate (Magnesium sulfate crystals can incorporate water molecules during the precipitation process depending on the ambient conditions. This results in various hydrated stages of the formed crystal, e.g. Magnesium sulfate heptahydrate (MgSO4.7H2O). For details see "magnesium sulfate".) (InChICode: 1S/Mg.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2) (SmilesCode: [Mg+2].[O-]S([O-])(=O)=O) (IUPAC Name: Magnesium sulfate) silicon dioxide (InChICode: 1S/O2Si/c1-3-2) (SmilesCode: O=[Si]=O) (IUPAC Name: Silicon dioxide)

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