micro-XRCT dataset of Enzymatically Induced Calcite Precipitation (EICP) in a microfluidic cell

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Vahid Dastjerdi, Samaneh; Steeb, Holger; Ruf, Matthias; Lee, Dongwon; Weinhardt, Felix; Karadimitriou, Nikolaos; Class, Holger, 2021, "micro-XRCT dataset of Enzymatically Induced Calcite Precipitation (EICP) in a microfluidic cell", https://doi.org/10.18419/darus-866, DaRUS, V1

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Description	micro-XRCT dataset (projection and reconstructed images) based on a region of interest scan (diameter 12.49 mm, height 9.09 mm) of a microfluidic cell including calcium carbonate aggregates along with the processed dataset (cropped, transformed and binarized).
Subject	Computer and Information Science; Earth and Environmental Sciences; Engineering
Keyword	Enzymatically Induced Calcite Precipitation, Micro X-Ray Computed Tomography (micro-XRCT), Porous Media
Related Publication	Weinhart, F., Class, H., Vahid Dastjerdi, S., Karadimitriou, N., Lee, D., & Steeb, H. (2021). Experimental Methods and Imaging for Enzymatically Induced Calcite Precipitation in a microfluidic cell. Water Resources Research, Technical Reports: Methods. doi: 10.1029/2020WR029361
Data Generation	Experiment
License/Data Use Agreement	CC BY 4.0

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	processed.tar TAR Archive - 2.6 MB Published Mar 11, 2021 34 Downloads MD5: d1931812fadb61cb603eab992e8542db This dataset is the transformed, cutted and processed version of the XRCT images. It contains the 20 binarized slices with the precipitates flagged as 1. The size of the volume is 89 mm x 22 mm x 0.085 mm.	Access File File Access Public Download Options TAR Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	projections.tar TAR Archive - 22.8 GB Published Mar 11, 2021 114 Downloads MD5: 857866c0fe383c5d7c991553b8aa3fbf Projection images (360 deg, angle increment 0.25 deg), dark image (di) and open beam image (ob) in 16 bit *.tif file format.	Access File File Access Public Download Options TAR Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	reconstructed.tar TAR Archive - 34.4 GB Published Mar 11, 2021 28 Downloads MD5: 1bc826ffd15ae7f4ea9a7d7eebbc756d Reconstructed micro-XRCT data set in 16 bit *.tif file format. 2940x2940x2139 voxels with the uniform voxel size of 4.24 µm.	Access File File Access Public Download Options TAR Archive Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/darus-866
Publication Date	2021-03-11
Title	micro-XRCT dataset of Enzymatically Induced Calcite Precipitation (EICP) in a microfluidic cell
Author	Vahid Dastjerdi, Samaneh (University of Stuttgart, Institute of Applied Mechanics (CE)) - ORCID: 0000-0003-0315-4067 Steeb, Holger (University of Stuttgart, Institute of Applied Mechanics (CE) & SimTech) - ORCID: 0000-0001-7602-4920 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)) - ORCID: 0000-0002-5359-7803 Weinhardt, Felix (University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems (IWS)) - ORCID: 0000-0002-1758-9427 Karadimitriou, Nikolaos (University of Stuttgart, Institute of Applied Mechanics (CE)) - ORCID: 0000-0002-9461-6214 Class, Holger (University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems (IWS)) - ORCID: 0000-0002-4476-8017
Point of Contact	Use email button above to contact. Steeb, Holger (University of Stuttgart, Institute of Applied Mechanics (CE) & SimTech)
Description	micro-XRCT dataset (projection and reconstructed images) based on a region of interest scan (diameter 12.49 mm, height 9.09 mm) of a microfluidic cell including calcium carbonate aggregates along with the processed dataset (cropped, transformed and binarized).
Subject	Computer and Information Science; Earth and Environmental Sciences; Engineering
Keyword	Enzymatically Induced Calcite Precipitation Micro X-Ray Computed Tomography (micro-XRCT) Porous Media https://www.wikidata.org/wiki/Q3271208 (Wikidata)
Related Publication	Weinhart, F., Class, H., Vahid Dastjerdi, S., Karadimitriou, N., Lee, D., & Steeb, H. (2021). Experimental Methods and Imaging for Enzymatically Induced Calcite Precipitation in a microfluidic cell. Water Resources Research, Technical Reports: Methods. doi: 10.1029/2020WR029361 https://doi.org/10.1029/2020WR029361
Language	English
Producer	Chair for Continuum-Mechanics (University of Stuttgart, Institute of Applied Mechanics (CE)) https://www.mib.uni-stuttgart.de/en SimTech Cluster of Excellence (University of Stuttgart) https://www.simtech.uni-stuttgart.de
Production Location	University of Stuttgart, Institute of Applied Mechanics (CE), Stuttgart, 70569, Germany
Contributor	Data Collector : Vahid Dastjerdi, Samaneh Related Person : Ruf, Matthias Related Person : Lee, Dongwon Rights Holder : Steeb, Holger
Funding Information	DFG: SFB 1313 - 327154368 DFG: EXC 2075 - 390740016
Project	SFB1313 - C04 - Control-volume-based approaches to model flow and transport in fractured/fracturing porous media including biological and chemical pore-space alteration
Depositor	Vahid Dastjerdi, Samaneh
Deposit Date	2020-08-05
Data Type	Image data
Related Dataset	Weinhardt, F., Class, H., Vahid Dastjerdi, S., Karadimitriou, N., Lee, D., & Steeb, H. (2021). Optical Microscopy and pressure measurements of Enzymatically Induced Calcite Precipitation (EICP) in a microfluidic cell. DaRUS. https://doi.org/10.18419/darus-818
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	Standard cone beam scanning of the centered sample (scan time: 15:46:00) Image Processing (Explained in: Weinhart, F., Class, H., Vahid Dastjerdi, S., Karadimitriou, N., Lee, D., & Steeb, H. (2021). Experimental Methods and Imaging for Enzymatically Induced Calcite Precipitation in a microfluidic cell. Water Resources Research, Technical Reports: Methods. https://doi.org/10.1029/2020WR029361)
Method Parameters	Geometric magnification [-] : 11.6533 Source object distance [mm] : 85.2129 Source detector distance [mm] : 993.008 X-ray tube voltage [kV] : 80 X-ray tube current [μA] : 100 Number of vertical detector pixel [pixel] : 2304 Number of horizontal detector pixel [pixel] : 2940 Detector pixel size [μm] : 49.5 Resulting voxel size [μm] : 4.24 Detector exposure time [ms] : 3000 Number of projection angles : 1800 Number of projections per angle : 1 Detector good pixel map : Version_ShadoBox6KHS_v2019-07-24 Detector in-plane (YZ-plane) moving pattern : [(0,0),(33,33),(33,-33),(-33,33),(-33,-33)] [pixel] Detector in-plane (YZ-plane) positions according to moving pattern : 5 Number of dark images(di) : 1 Number of open beam images(ob) : 1 Position X-axis [mm] : 271.5 Position Y-axis [mm] : 14.65 Position Z-axis [mm] : 25.6975 Position x-axis [mm] : 2.2 Position y-axis [mm] : -2 Position switch detector axis [mm] : 452 Position detector X-axis [mm] : 10 Position detector Y-axis [counts] : 298400 Position detector Z-axis [counts] : 179240
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) MATLAB Version: 2019b (MATLAB 2019b, 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: "ShadoBox6KHS_v2019-11-11" Detector , Version: Shad-o-Box 6K HS with CsI scintillator

Engineering Metadata

Data Generation	Experiment
System Phases	microfluidic cells (Components: Poly-Di-Methyl-Siloxane (PDMS)) Calcium Carbonate aggregates (Components: CaCO3)

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