Dataset DOI: 10.5061/dryad.v41ns1s91

Description of the data and file structure

This dataset contains the raw data acquired in the study "The Effects of Carbonate Precipitation on the Physical Properties of Basalt". The raw data come in three main formats: X-Ray computed tomography (CT) images, binary waveform files for ultrasonic data, and data recorded by the suite of auxiliary sensors used in the experiment (e.g., fluid pressure, pump flow rate, outlet sensor flow rate, etc.). Each data type and how it can be used is explained below.

Time-lapse CT Data

The timelapse CT data comes in the format of a stack of .tiff images. These images are the product of 3D reconstruction and processing from Nikon and VisualStudio Max software. Each 3D rock scan is composed of approximately 2000 individual horizontal slices, which, when stacked together, form a 3D volume. The pixel/voxel spacing for all scans is 11.5 micron (although exact dimensions can be found in the json file associated with each scan).

Processing of the CT data was performed mainly using the open source software package 3D Slicer (see here) running on a Linux Ubuntu OS. The ANTs registration module was used within 3D Slicer for volume registration/alignment, and can be downloaded as a plugin from the module downloader wizard within Slicer. The processing workflow was largely automated using the Python interface that can be run within Slicer. The workflow script which handled most of this automatic workflow for processing timelapse CT data is included in the scripts directory.

Waveform Data

Ultrasonic waveform data is included for the relevant experiments. Ultrasonic waveforms are saved in NumPy .npy binary format. The time of acquisition is included in the file name (as Unix time), along with the trigger delay in percent of the record (td) and the sampling interval in ns (si). Each NumPy file contains either 2 or 4 channels in a structured array format, which is accessible using the dtype names as fields (dtype names can be determined by accessing the array.dtype.names field). The channel voltage level is contained in each heading for each channel so that the integer data can be converted into voltages.

Sensor Data

The third type of data included here are the remaining data acquired by the sensors in the experiment. These include the outlet flow rate sensor, upstream pressure, pump flow rate, and ambient temperature. Each of these datasets is saved in .npy format in a structured array, with the time of acquisition recorded in the first columns. In addition, a .json file has information that explains the acquisition state for each experiment and has comments on the experimental setup. Note that some experiments have multiple folders of sensor data as the recording software had to be restarted multiple times during the course of the experiment. 

Files and variables

Directory Structure

.
├── B31
│   ├── experiment_data
│   │   └── sensorview_data
│   │       └── b31_calcite_precip_sodium-carbonate
│   │           ├── ArduinoSLF3x
│   │           │   └── b31_calcite_precip_sodium-carbonate_experiment-data_2024-05-23_17-00-36_ArduinoSLF3x.npy
│   │           ├── b31_calcite_precip_sodium-carbonate_experiment-config_2024-05-23_17-00-36.json
│   │           ├── Permeability
│   │           │   └── b31_calcite_precip_sodium-carbonate_experiment-data_2024-05-23_17-00-36_Permeability.npy
│   │           └── SyringePumpPID
│   │               └── b31_calcite_precip_sodium-carbonate_experiment-data_2024-05-23_17-00-36_SyringePumpPID.npy
│   └── waveforms
│       ├── b31_calcite_precip_sodium-carbonate_pulsing_ae_classifications.csv
│       ├── b31_calcite_precip_sodium-carbonate_waveform*.mat
│       ├── b31_calcite_precip_sodium-carbonate_waveform_si-0v8ns_td-50v*.npy
├── B32
│   ├── CT
│   │   ├── B32_bubbles_volumes_sensor-locations.csv
│   │   ├── B32_calcite_volumes_full_master.csv
│   │   └── ImageStacks_B32_adjusted
│   │       ├── scan[0-38]_lvl6700_win7500
│   │       │   ├── B32_sodium-carbonate_precip_*.tif
│   │       ├── scan_Dry_PreExp_lvl6700_win7500
│   │       │   ├── B32_sodium-carbonate_precip_scan_Dry_PreExp_*.tif
│   │       └── scan_VacuumOvenDry_PostExp_HighRes_lvl6700_win7500
│   │           ├── B32_sodium-carbonate_precip_scan_VacuumOvenDry_PostExp_HighRes_*.tif
│   ├── experiment_data
│   │   └── sensorview_data
│   │       ├── B32_sodium-carbonate_CT-1[-1-57]
│   │       │   ├── ArduinoSLF3x
│   │       │   │   └── B32_sodium-carbonate_CT-1*_experiment-data_*_ArduinoSLF3x.npy
│   │       │   ├── B32_sodium-carbonate_CT-1*_experiment-config_*.json
│   │       │   ├── Permeability
│   │       │   │   └── B32_sodium-carbonate_CT-1*_experiment-data_*_Permeability.npy
│   │       │   └── SyringePumpPID
│   │       │       └── B32_sodium-carbonate_CT-1*_experiment-data_*_SyringePumpPID.npy
│   └── waveforms
│       ├── 20250115-0001_si-2v0ns_td-50v003997us_npy_*.npy
│       └── b32_calcite_precip_sodium-carbonate_pulsing_ae_classifications.csv
├── B35
│   └── experiment_data
│       └── sensorview_data
│           ├── B35_sodium-carbonate_precip_CT1[-1-13]
│           │   ├── ArduinoSLF3x
│           │   │   └── B35_sodium-carbonate_precip_CT1*_experiment-data_*_ArduinoSLF3x.npy
│           │   ├── B35_sodium-carbonate_precip_CT1*_experiment-config_*.json
│           │   ├── Permeability
│           │   │   └── B35_sodium-carbonate_precip_CT1*_experiment-data_*_Permeability.npy
│           │   └── SyringePumpPID
│           │       └── B35_sodium-carbonate_precip_CT1*_experiment-data_*_SyringePumpPID.npy
├── B37
│   ├── CT
│   │   ├── IcelandicBasalt_JS_B37_post_01_tifStack
│   │   │   ├── IcelandicBasalt_JS_B37_post_01_*.tif
│   │   └── IcelandicBasalt_JS_B37_pre_01_tifStack
│   │       ├── IcelandicBasalt_JS_B37_pre_01_*.tif
│   ├── experiment_data
│   │   └── sensorview_data
│   │       ├── b37_calcite_precip_sodium-carbonate-[8-10]*
│   │       │   ├── AirPressureAndTemperature
│   │       │   │   └── b37_calcite_precip_sodium-carbonate_experiment-data_*_AirPressureAndTemperature.npy
│   │       │   ├── ArduinoSLF3x
│   │       │   │   └── b37_calcite_precip_sodium-carbonate_experiment-data_*_ArduinoSLF3x.npy
│   │       │   ├── b37_calcite_precip_sodium-carbonate_experiment-config_*.json
│   │       │   ├── Permeability
│   │       │   │   └── b37_calcite_precip_sodium-carbonate_experiment-data_*_Permeability.npy
│   │       │   └── SyringePumpPID
│   │       │       └── b37_calcite_precip_sodium-carbonate_experiment-data_*_SyringePumpPID.npy
│   └── waveforms
│       ├── b37_calcite_precip_sodium-carbonate_pulsing_ae_classifications.csv
│       ├── b37_calcite_precip_sodium-carbonate_waveform*.mat
│       ├── b37_calcite_precip_sodium-carbonate_waveform_si-0v8ns_td-*_npy_*.npy
├── B41
│   ├── CT
│   │   ├── B41_calcite_volumes_full_thr25.csv
│   │   ├── B41_calcite_volumes_pore1549.csv
│   │   ├── B41_calcite_volumes_pore3224.csv
│   │   ├── B41_calcite_volumes_pore6036.csv
│   │   ├── B41_calcite_volumes_pore8864.csv
│   │   ├── B41_calcite_volumes_sensors.csv
│   │   └── ImageStacks_B41_adjusted
│   │       ├── scan[1-59]_lvl8000_win7168
│   │       │   ├── B41_sodium-carbonate_precip_scan[1-59]_*.tif
│   │       ├── scan_Dry_PostExp_lvl8000_win7168
│   │       │   ├── B41_sodium-carbonate_precip_scan_Dry_PostExp_*.tif
│   │       └── scan_Dry_PreExp_lvl8000_win7168
│   │           ├── B41_sodium-carbonate_precip_scan_Dry_PreExp_*.tif
│   ├── experiment_data
│   │   └── sensorview_data
│   │       ├── B41_after24_P*
│   │       │   ├── ArduinoSLF3x
│   │       │   │   └── B41_*_experiment-data_*_ArduinoSLF3x.npy
│   │       │   ├── B41_*_experiment-config_*.json
│   │       │   ├── Permeability
│   │       │   │   └── B41_*_experiment-data_*_Permeability.npy
│   │       │   └── SyringePumpPID
│   │       │       └── B41_*_experiment-data_*_SyringePumpPID.npy
│   │       ├── B41_sodium-carbonate_CT
│   │       │   ├── ArduinoSLF3x
│   │       │   │   └── B41_sodium-carbonate_CT_experiment-data_2025-03-27_15-56-06_ArduinoSLF3x.npy
│   │       │   ├── B41_sodium-carbonate_CT_experiment-config_2025-03-27_15-56-06.json
│   │       │   ├── Permeability
│   │       │   │   └── B41_sodium-carbonate_CT_experiment-data_2025-03-27_15-56-06_Permeability.npy
│   │       │   └── SyringePumpPID
│   │       │       └── B41_sodium-carbonate_CT_experiment-data_2025-03-27_15-56-06_SyringePumpPID.npy
│   │       └── B41_sodium-carbonate_CT_post-24hr
│   │           ├── ArduinoSLF3x
│   │           │   └── B41_sodium-carbonate_CT_post-24hr_experiment-data_2025-03-28_16-56-51_ArduinoSLF3x.npy
│   │           ├── B41_sodium-carbonate_CT_post-24hr_experiment-config_2025-03-28_16-56-51.json
│   │           ├── Permeability
│   │           │   └── B41_sodium-carbonate_CT_post-24hr_experiment-data_2025-03-28_16-56-51_Permeability.npy
│   │           └── SyringePumpPID
│   │               └── B41_sodium-carbonate_CT_post-24hr_experiment-data_2025-03-28_16-56-51_SyringePumpPID.npy
│   └── waveforms
│       ├── 20250327-0001_si-*ns_td-*us_npy_*.npy
│       └── b41_calcite_precip_sodium-carbonate_pulsing_ae_classifications.csv
├── manuals
│   └── worksflow_for_3d-slicer_ct_processing.odt
└── scripts
    ├── ct_scripts
    │   ├── adjust_levels_and_equalize.py
    │   ├── calculate_porosity.py
    │   ├── calculate_precipitate_volume_in_zones.py
    │   ├── calculate_precipitate_volume.py
    │   ├── count_nonzero_pixels.ijm
    │   ├── output_animation.txt
    │   └── slicer_process_timelapse_scans.py
    └── waveform_scripts
        ├── b37_calcite_precip_ultrasonics_proc.py
        ├── helper_functions.py
        └── __pycache__

Folders, Files, and Variables

The experimental data is stored in the folder corresponding to each sample number (B31, B32, B35, B37, and B41). Within each sample folder, there are one or more folders titled experiment_data, waveforms, and/or CT.

experiment_data

The experiment data folders contain the "sensorview_data" files which record the data from the sensors used in each experiment (e.g. permeability, flow rate, experiment configuration, etc.), as described in the "Sensor Data" section above. There are often multiple folders in the "sensorview_data" folder, as the acquisition program sometimes had to be restarted multiple times over the course of a single experiment. The order that these individual acquisitions were acquired is given in the folder/file names, and these data can be stitched together to obtain the full sensor data over the course of the experiment.

waveforms

These folders contain the waveform data, as described above. In addition, each waveform folder contains a csv file which is named* ...pulsing_*ae_classifications.csv. This is a tabulated list of all the waveform files recorded, with the headers:

file_index: The waveform file number in order of recording

file_name: The full name of the waveform file, with the UNIX time stamp of recording

waveform_type: This is either "pulse" or "ae", referring to active pulsing of the ultrasonic sensors or a passive acoustic emission. The vast majority of waveforms are pulses.

CT

These folders contain the semi-processed micro X-Ray CT images in tiff format. Each sub-folder corresponds to an individual scan. Pre- and Post- experiment scans are identified in their folder names. These are longer-duration (~2 hr) scans performed before and after the experiments. Folders that have "scan*" in their name (where star is a number from 0-59) correspond to short-duration (6-12 min) scans performed during the flow-through experiments. In most cases, these data have been pre-processed to equalize the grey values/histograms across all scans in an experiment. The adjusted midpoint and window of the histograms for each image are given by the lvl and win numbers in the folder names.

In addition to the folders containing the tif files, there are several .csv files containing tabulated data from the processing steps of the CT data in some of the CT folders. These all contain the volumes of precipitates for each scan either for the full sample or individual pores (as identified in the file name). The variables in each of these files are as follows:

scan_name: The name of the scan

unix_time: The time the scan was started in seconds since the epoch

relative_time: Number of elapsed seconds to the start of the scan since the first scan

readable_time: A readable timestamp for the start time of each scan

calcite_volume_voxels: The number of voxels within the scan that were above the threshold identified for precipitates. The threshold for each experiment was constant, and is identified in the file name of each csv file.

calcite_volume_cm3: The total volume of precipitates in cubic centimeters.

Code/software

Example scripts used in the processing of these data are included in the scripts directory. The description of the function of each script is included in the headers of each file. 3D Slicer, FIJI/ImageJ (using the 3D Script plugin), and Python were used extensively to process and analyze this data. A processing workflow written in Python is included (slicer_process_timelapse_scans.py) that runs within 3D Slicer to automate many of the tasks of processing the CT data.

Manuals

A detailed manual describing the processing steps in 3D slicers is included in the manuals directory. This processing workflow is implemented in the processing workflow script (slicer_process_timelapse_scans.py).