Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of high column (sample 4) (doi:10.18419/darus-2907)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of high column (sample 4)

Identification Number:

doi:10.18419/darus-2907

Distributor:

DaRUS

Date of Distribution:

2022-07-12

Version:

1

Bibliographic Citation:

Ruf, Matthias; Hommel, Johannes; Steeb, Holger, 2022, "Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of high column (sample 4)", https://doi.org/10.18419/darus-2907, DaRUS, V1, UNF:6:ZBzSpg62B7xn5d+OtyUilg== [fileUNF]

Study Description

Citation

Title:

Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of high column (sample 4)

Identification Number:

doi:10.18419/darus-2907

Authoring Entity:

Ruf, Matthias (University of Stuttgart, Institute of Applied Mechanics (CE))

Hommel, Johannes (University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems)

Steeb, Holger (University of Stuttgart, Institute of Applied Mechanics (CE) & SC SimTech)

Other identifications and acknowledgements:

Steeb, Holger

Producer:

University of Stuttgart, Institute of Applied Mechanics (CE) - Chair for Continuum-Mechanics

University of Stuttgart - Cluster of Excellence EXC 2075 "SimTech"

Date of Production:

2020

Grant Number:

357361983

Grant Number:

EXC 2075 - 390740016

Grant Number:

SFB 1313 ‐ 327154368

Grant Number:

380443677

Distributor:

DaRUS

Access Authority:

Steeb, Holger

Holdings Information:

https://doi.org/10.18419/darus-2907

Study Scope

Keywords:

Chemistry, Computer and Information Science, Earth and Environmental Sciences, Engineering, Enzymatically Induced Calcium Carbonate Precipitation, Biomineralization, Porous Media, Micro X-Ray Computed Tomography (micro-XRCT), X-ray Microtomography

Abstract:

This dataset contains micro X-ray Computed Tomography (micro-XRCT) data sets (projection, reconstructed, and segmented images) from a sintered glass beads column packing with enzymatically induced carbonate precipitation. The prepared sintered glass beads column sample has a diameter of about 5 mm and a length of 10 mm. It consists of glass beads with a diameter of about 180 µm which were sintered. For the subsequent mineralization procedure, the sample was sealed on the side with a shrink tube and glued into the center of a cylindrical, 3D-printed plastic mold using epoxy resin. For further details, see Gehring et al. (2022).<br><br> For the carbonate precipitation, the sample was put into a sample holder with three separate inlets: one for pressure measurement and two for separate injection of the urease solution (at 5 kg/m³) and the mineralization solution (containing calcium and urea at 333 mol/m³ concentrations each) and one outlet. The pressure was measured to monitor the progress of mineralization. Mineralization was carried out at 60°C to increase the reaction rates of urea hydrolysis and calcium carbonate precipitation. The reaction solutions were injected into the sample at a rate of 5 µl/s each initially using syringe pumps with a total volume of 5 ml, necessitating refilling of the syringes between injection periods. Mineralization was continued until the maximum pressure of 8 bar was reached. For this experiment, the injection rate was step-wise decreased during the course of the experiment as the maximum pressure was reached and the experiment then continued. The mineralization was carried out over the course of three days. At each following day, the mineralization was continued with the highest possible determined injection rate &le;5 µl/s each, the minimum final injection rate was 0.5 µl/s each. During the mineralization, the applied injection rates of both solutions and the measured pressure were recorded and are provided for each day as *.csv file ("Column4_highMineralization_20190926.csv", "Column4_highMineralization_20190927.csv", "Column4_highMineralization_20191030.csv").<br><br> The micro-XRCT scan data include an overview scan of the entire sample (projections_overview.tar.gz; reconstructed_overview.tar.gz), as well as a scan focused on the inlet section (projections_inlet.tar.gz; reconstructed_inlet.tar.gz), and the outlet section (projections_outlet.tar.gz; reconstructed_outlet.tar.gz). The inlet section of the sample is located at the top side of the glass beads column. Image stack counting from top to bottom.<br><br> Based on the reconstructed gray-values data set of the sample outlet ("reconstructed_outlet.tar.gz"), a segmentation ("segmentedPNGs_outlet.tar.gz") into three phases was performed: glass beads, precipitated calcium carbonate, and pore space.<br><br> For this, first, the software ilastik was used to get a distribution of the probabilities of identification of each voxel to those three phases, which were expressed as color values: red = glass beads, blue = precipitated calcium carbonate, and green = pore space. In a second step, based on the output by ilastik ("probabilities_outlet.tar.gz"), the software Matlab (see the Matlab script "column_postprocess.m" in "segmentedPNGs_outlet.tar.gz") was used to finalize the segmentation assigning each voxel to a single-phase and to crop out an inner subvolume undisturbed by irregularities at the outer edges of the sample. The resulting binarized stacks of images of each of the phases are given: glass beads ("segmentedPNGs_outlet.tar.gz", subfolder "red_sand"), precipitated calcium carbonate ("segmentedPNGs_outlet.tar.gz", subfolder "blue_precip"), pore space ("segmentedPNGs_outlet.tar. gz", subfolder "green_void"), as well as precipitate and pore space representing the initial, unmineralized pore space, ("segmentedPNGs_outlet.tar.gz", subfolder "precip_plus_void"), in which white signifies the presence of the respective phase at the location and black absence of the respective phase.

Kind of Data:

Image data

Notes:

Ruf, M. and Hommel, J. contributed equally.

Methodology and Processing

Sources Statement

Data Access

Other Study Description Materials

Related Studies

Hommel, J. & Weinhardt, F. (2022). Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - microfluidics samples. DaRUS. <a href="https://doi.org/10.18419/darus-2791">https://doi.org/10.18419/darus-2791</a>

<br>Hommel, J. & Gehring, L. (2022). Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - column samples. DaRUS. <a href="https://doi.org/10.18419/darus-1713">https://doi.org/10.18419/darus-1713</a>

<br>Ruf, M., Hommel, J. & Steeb, H. (2022). Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of medium column (sample 3). DaRUS. <a href="https://doi.org/10.18419/darus-2906">https://doi.org/10.18419/darus-2906</a>

<br>Ruf, M., Hommel, J. & Steeb, H. (2022). Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - micro-XRCT dataset of low column (sample 10). DaRUS. <a href="https://doi.org/10.18419/darus-2908">https://doi.org/10.18419/darus-2908</a>

Related Publications

Citation

Title:

Gehring, L., Weinhardt, F., Ruf, M., Hommel, J. & Steeb, H. (2022). Effects of enzymatically induced carbonate precipitation on capillary pressure-saturation relations. <em>Minerals</em>, 12(10), 1186.

Identification Number:

10.3390/min12101186

Bibliographic Citation:

Gehring, L., Weinhardt, F., Ruf, M., Hommel, J. & Steeb, H. (2022). Effects of enzymatically induced carbonate precipitation on capillary pressure-saturation relations. <em>Minerals</em>, 12(10), 1186.

Other Reference Note(s)

Ruf, M., & Steeb, H., (2020). An open, modular, and flexible micro X-ray computed tomography system for research. <em>Review of Scientific Instruments</em>, 91(11), 113102. <a href="https://doi.org/10.1063/5.0019541">https://doi.org/10.1063/5.0019541</a>

File Description--f133001

File: Column4_highMineralization_20190926.tab

  • Number of cases: 10145

  • No. of variables per record: 5

  • Type of File: text/tab-separated-values

Notes:

UNF:6:z5CcGPSe70fw3C4FClKdyw==

File Description--f133003

File: Column4_highMineralization_20190927.tab

  • Number of cases: 8636

  • No. of variables per record: 5

  • Type of File: text/tab-separated-values

Notes:

UNF:6:EsUGRQAiVK28EW7tApTvbw==

File Description--f133002

File: Column4_highMineralization_20191030.tab

  • Number of cases: 8805

  • No. of variables per record: 5

  • Type of File: text/tab-separated-values

Notes:

UNF:6:wfSQfH/TdRKvPFz7VdOJFg==

Variable Description

List of Variables:

Variables

Time (s)

f133001 Location:

Summary Statistics: Max. 10144.0; Mean 5072.0; StDev 2928.753574474985; Min. 0.0; Valid 10145.0

Variable Format: numeric

Notes: UNF:6:imcPGZ7XGC7uuIssY4SxqA==

Abs.Timestamp

f133001 Location:

Variable Format: character

Notes: UNF:6:Hy3rvoXqSmehSd4/VFQDqQ==

Delta p [bar]

f133001 Location:

Variable Format: character

Notes: UNF:6:JTlWXCIXcr1aOlNaU3KafQ==

Urease solution [ml/s]

f133001 Location:

Variable Format: character

Notes: UNF:6:ljWSFqr63tMmIygJekCkOQ==

Urea & calcium solution [ml/s]

f133001 Location:

Variable Format: character

Notes: UNF:6:HUsfJ/ZNxJ2XwNI07dIrJQ==

Time (s)

f133003 Location:

Summary Statistics: Mean 4317.5; Max. 8635.0; Min. 0.0; Valid 8636.0; StDev 2493.1427957499745

Variable Format: numeric

Notes: UNF:6:mG9fxWubeDr15GRUIkp4rw==

Abs.Timestamp

f133003 Location:

Variable Format: character

Notes: UNF:6:0PAbFeIAYevovARNCVZLNg==

Delta p [bar]

f133003 Location:

Variable Format: character

Notes: UNF:6:f1f3ZMwjSLhqZbMi4A8ecQ==

Urease solution [ml/s]

f133003 Location:

Variable Format: character

Notes: UNF:6:j8CoUPo/DBx9i3alKsbRXQ==

Urea & calcium solution [ml/s]

f133003 Location:

Variable Format: character

Notes: UNF:6:KVdsIo/U4pZvKuwOFs5mDA==

Time (s)

f133002 Location:

Summary Statistics: StDev 2541.928893576687; Mean 4402.0; Min. 0.0; Max. 8804.0; Valid 8805.0;

Variable Format: numeric

Notes: UNF:6:ViSGQ+P9d2nMDllxgdOT6g==

Abs.Timestamp

f133002 Location:

Variable Format: character

Notes: UNF:6:JjZoWMG4GEjqTrypGKJhkw==

Delta p [bar]

f133002 Location:

Variable Format: character

Notes: UNF:6:iWvVDTla5VvdMWkp2F7uUA==

Urease solution [ml/s]

f133002 Location:

Variable Format: character

Notes: UNF:6:Nv5fNVJrtvVZR1SOvyDXeg==

Urea & calcium solution [ml/s]

f133002 Location:

Variable Format: character

Notes: UNF:6:r811KaDrdPJgL5YNT0Mh5Q==

Other Study-Related Materials

Label:

projections_inlet.tar.gz

Text:

Projection images (360 deg, angle increment 0.20 deg), dark image (di) and open beam image (ob) in 16 bit *.tif file format of the specimen inlet (internal ID: 20200123_01/projections)

Notes:

application/gzip

Other Study-Related Materials

Label:

reconstructed_inlet.tar.gz

Text:

Reconstructed micro-XRCT data set in 16 bit *.tif file format of the specimen inlet. 2940x2940x2129 voxels with a uniform voxel size of 2.2 µm. (internal ID: 20200123_01/reconstructed)

Notes:

application/gzip

Other Study-Related Materials

Label:

probabilities_outlet.tar.gz

Text:

ilastik output: probabilities of phase identifiactions: red = glass beads, blue = precipitated calcium carbonate, green = pore space. In 24 bit *.png file format. 2680x2680x2141 voxels with a uniform voxel size of 2.2 µm.

Notes:

application/gzip

Other Study-Related Materials

Label:

projections_outlet.tar.gz

Text:

Projection images (360 deg, angle increment 0.20 deg), dark image (di) and open beam image (ob) in 16 bit *.tif file format of the specimen outlet (internal ID: 20200124_01/projections)

Notes:

application/gzip

Other Study-Related Materials

Label:

reconstructed_outlet.tar.gz

Text:

Reconstructed micro-XRCT data set in 16 bit *.tif file format of the specimen outlet. 2940x2940x2139 voxels with a uniform voxel size of 2.2 µm. (internal ID: 20200124_01/reconstructed)

Notes:

application/gzip

Other Study-Related Materials

Label:

segmentedPNGs_outlet.tar.gz

Text:

Binarized images of the probabilities into glass beads, precipitated calcium carbonate, and pore space, as well as precipitated calcium carbonate and pore space (= initial pore space), each in a subfolder. In 8 bit *.png file format. 2682x2682x1340 voxels with a uniform voxel size of 2.2 µm.

Notes:

application/gzip

Other Study-Related Materials

Label:

projections_overview.tar.gz

Text:

Projection images (360 deg, angle increment 0.20 deg), dark image (di) and open beam image (ob) in 16 bit *.tif file format of the entire specimen (internal ID: 20200122_01/projections)

Notes:

application/gzip

Other Study-Related Materials

Label:

reconstructed_overview.tar.gz

Text:

Reconstructed micro-XRCT data set in 16 bit *.tif file format of the entire specimen. 2940x2940x2139 voxels with a uniform voxel size of 6.0 µm. (internal ID: 20200122_01/reconstructed)

Notes:

application/gzip