!!!***** SAVE THIS FILE REGULARLY. CHANGES ARE NOT SAVED AUTOMATICALLY ****!!! [This template readme file should be edited to be relevant to your dataset. The template proposes a basic set of information to be provided about a dataset. Sections 1-3 provide key information about the dataset and should be completed as fully as possible; Sections 4-5 provide information for interpretation and use of the dataset, and should be completed according to your judgement. Ask yourself in completing these sections: what information would the user of this dataset need in order to be able to understand it or replicate the results? Use of the README plain text format for dataset documentation is not required, and may not be suitable for longer or more detailed documentation. In these cases, or if preferred, you can use PDF or MS Word. Information provided here must correspond accurately with information provided in the dataset metadata record, e.g. the dataset title should match exactly, the same Creators should be listed, etc. The readme file should be saved with the name README_[Creator surname]_[Publication year]. The file name should not exceed 32 characters. Examples: README_Smith_2025.txt; README_Jones-etal_2025.txt. Text within square brackets is instructional and should be deleted from the final version of the readme.] 1. ABOUT THE DATASET -------------------- Title: In situ observation of effects of surface chemistry towards calcium carbonate crystallisation in confinement. Creator(s): Zhao Jiang [1], Maxime Durelle [1], Raphael Stone [1], Adriana Matamoros Veloza [1], Xiaoyue Wu [1], Dario Ferreira Sanchez [2], Pierre-Olivier Autran [3], Jonathan Wright [3], Yi-Yeoun Kim [1], Fiona Meldrum [1] Organisation(s): 1. University of Leeds. 2. Paul Scherrer Institut. 3. European Synchrotron Radiation Facility. Rights-holder(s): Unless otherwise stated, Copyright 2026 University of Leeds Publication Year: 2026 Description: This dataset comprises two categories of volumetric imaging data: diffraction tomograms and absorption tomograms. File naming follows a structured convention encoding the experimental conditions in the format: compound–surface functionalisation–initial solution concentration–scan number. Three compound systems are included under XRD-CT measurements: calcium carbonate (target system), calcium chloride, and water (both serving as controls). Controlled pore glass (CPG) rods were prepared with three surface chemistries: COOH-functionalised, NH₂-functionalised, and native (unmodified). Experiments were conducted at two initial solution concentrations: 50 mM and 100 mM. Each XRD-CT scan is stored within a dedicated folder containing two primary data files: (i) a 3D sinogram in .h5 format, and (ii) a corresponding 1D XRD pattern in .xy format summarizing diffraction intensity profiles. Temporal information, including acquisition timestamps, is embedded within the metadata of the .h5 files. Cite as: Jiang, Zhao; Durelle, Maxime; Stone, Raphael; Matamoros Veloza, Adriana; Wu, Xiaoyue; Ferreira Sanchez, Dario; Autran, Pierre-Olivier; Wright, Jonathan; Kim, Yi-Yeoun and Meldrum, Fiona (2026) Dataset for 'In situ observation of effects of surface chemistry towards calcium carbonate crystallisation in confinement'. University of Leeds. [Dataset] https://doi.org/10.5518/1843 Related publication: Jiang, Zhao; Durelle, Maxime; Stone, Raphael; Matamoros Veloza, Adriana; Wu, Xiaoyue; Ferreira Sanchez, Dario; Autran, Pierre-Olivier; Wright, Jonathan; Kim, Yi-Yeoun and Meldrum, Fiona, In situ observation of effects of surface chemistry towards calcium carbonate crystallisation in confinement, in preparation Contact: violetchiang0621@gmail.com 2. TERMS OF USE --------------- Copyright 2026 University of Leeds. This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 3. PROJECT AND FUNDING INFORMATION ---------------------------------- Title: DYNAMIN Dates: September 2018 – August 2025 Funding organisation: European Research Council (ERC) Grant no.: 788968 Title: Crystallisation in the Real World: Delivering Control through Theory and Experiment Dates: March 2018 – March 2025 Funding organisation: Engineering and Physical Sciences Research Council (EPSRC) Grant no.: EP/R018820/1 Title: Chinese Scholarship Committee Dates: September 2021 – August 2024 Funding organisation: Chinese Scholarship Committee 4. CONTENTS ----------- File listing FILE STRUCTURE ============== /Diffraction_Tomograms/ │ │ Each scan folder contains two files: │ *_3dsinogram.h5 — 3D sinogram with embedded acquisition timestamps │ *_sum.xy — 1D integrated XRD intensity profile │ ├── CaCO3_COOH_100mM/ │ ├── Scan_0001/ Aug_CaCO3_COOH_100mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_100mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_COOH_100mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_100mM_2_xrdct_scan_xrd_sum.xy │ ├── Scan_0003/ Aug_CaCO3_COOH_100mM_3_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_100mM_3_xrdct_scan_xrd_sum.xy │ ├── Scan_0004/ Aug_CaCO3_COOH_100mM_4_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_100mM_4_xrdct_scan_xrd_sum.xy │ ├── Scan_0005/ Aug_CaCO3_COOH_100mM_5_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_100mM_5_xrdct_scan_xrd_sum.xy │ └── Scan_0006/ Aug_CaCO3_COOH_100mM_6_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_COOH_100mM_6_xrdct_scan_xrd_sum.xy │ ├── CaCO3_COOH_50mM/ │ ├── Scan_0001/ Aug_CaCO3_COOH_50mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_COOH_50mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_2_xrdct_scan_xrd_sum.xy │ ├── Scan_0003/ Aug_CaCO3_COOH_50mM_3_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_3_xrdct_scan_xrd_sum.xy │ ├── Scan_0004/ Aug_CaCO3_COOH_50mM_4_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_4_xrdct_scan_xrd_sum.xy │ ├── Scan_0005/ Aug_CaCO3_COOH_50mM_5_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_5_xrdct_scan_xrd_sum.xy │ ├── Scan_0006/ Aug_CaCO3_COOH_50mM_6_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_COOH_50mM_6_xrdct_scan_xrd_sum.xy │ └── Scan_0007/ Aug_CaCO3_COOH_50mM_7_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_COOH_50mM_7_xrdct_scan_xrd_sum.xy │ ├── CaCO3_Native_100mM/ │ ├── Scan_0001/ Aug_CaCO3_Native_100mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_100mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_Native_100mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_100mM_2_xrdct_scan_xrd_sum.xy │ └── Scan_0003/ Aug_CaCO3_Native_100mM_3_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_Native_100mM_3_xrdct_scan_xrd_sum.xy │ ├── CaCO3_Native_50mM/ │ ├── Scan_0001/ Aug_CaCO3_Native_50mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_50mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_Native_50mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_50mM_2_xrdct_scan_xrd_sum.xy │ ├── Scan_0003/ Aug_CaCO3_Native_50mM_3_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_50mM_3_xrdct_scan_xrd_sum.xy │ ├── Scan_0004/ Aug_CaCO3_Native_50mM_4_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_50mM_4_xrdct_scan_xrd_sum.xy │ ├── Scan_0005/ Aug_CaCO3_Native_50mM_5_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_Native_50mM_5_xrdct_scan_xrd_sum.xy │ └── Scan_0006/ Aug_CaCO3_Native_50mM_6_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_Native_50mM_6_xrdct_scan_xrd_sum.xy │ ├── CaCO3_NH2_100mM/ │ ├── Scan_0001/ Aug_CaCO3_NH2_100mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_100mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_NH2_100mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_100mM_2_xrdct_scan_xrd_sum.xy │ └── Scan_0003/ Aug_CaCO3_NH2_100mM_3_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_NH2_100mM_3_xrdct_scan_xrd_sum.xy │ ├── CaCO3_NH2_50mM/ │ ├── Scan_0001/ Aug_CaCO3_NH2_50mM_1_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_50mM_1_xrdct_scan_xrd_sum.xy │ ├── Scan_0002/ Aug_CaCO3_NH2_50mM_2_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_50mM_2_xrdct_scan_xrd_sum.xy │ ├── Scan_0003/ Aug_CaCO3_NH2_50mM_3_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_50mM_3_xrdct_scan_xrd_sum.xy │ ├── Scan_0004/ Aug_CaCO3_NH2_50mM_4_xrdct_scan_xrd_3dsinogram.h5 │ │ Aug_CaCO3_NH2_50mM_4_xrdct_scan_xrd_sum.xy │ └── Scan_0005/ Aug_CaCO3_NH2_50mM_5_xrdct_scan_xrd_3dsinogram.h5 │ Aug_CaCO3_NH2_50mM_5_xrdct_scan_xrd_sum.xy │ ├── Control_CaCl2_50mM/ │ └── Aug_Control_50mM_CaCl2_xrdct_scan_xrd_3dsinogram.h5 │ Aug_Control_50mM_CaCl2_xrdct_scan_xrd_sum.xy │ └── Control_H2O/ └── Aug_Control_H2O_xrdct_scan_xrd_3dsinogram.h5 Aug_Control_H2O_xrdct_scan_xrd_sum.xy /Tomograms/ │ │ Files are labelled tomo_[N] where [N] is the time point index │ within the experiment. Indices are not always consecutive, │ reflecting selective acquisition or retention of time points. │ ├── CaCO3_COOH_100mM/ (time points: 6, 7, 8, 9, 10) │ ├── Aug_CaCO3_COOH_100mM_1_tomo_6 │ ├── Aug_CaCO3_COOH_100mM_1_tomo_7 │ ├── Aug_CaCO3_COOH_100mM_1_tomo_8 │ ├── Aug_CaCO3_COOH_100mM_1_tomo_9 │ └── Aug_CaCO3_COOH_100mM_1_tomo_10 │ ├── CaCO3_COOH_50mM/ (time points: 1, 2, 4, 5) │ ├── Aug_CaCO3_COOH_50mM_2_tomo_1 │ ├── Aug_CaCO3_COOH_50mM_2_tomo_2 │ ├── Aug_CaCO3_COOH_50mM_2_tomo_4 │ └── Aug_CaCO3_COOH_50mM_2_tomo_5 │ ├── CaCO3_Native_100mM/ (time points: 6, 7) │ ├── Aug_CaCO3_Native_100mM_2_tomo_6 │ └── Aug_CaCO3_Native_100mM_2_tomo_7 │ ├── CaCO3_Native_50mM/ (time points: 1, 2, 4, 6) │ ├── Aug_CaCO3_Native_50mM_2_tomo_1 │ ├── Aug_CaCO3_Native_50mM_2_tomo_2 │ ├── Aug_CaCO3_Native_50mM_2_tomo_4 │ └── Aug_CaCO3_Native_50mM_2_tomo_6 │ ├── CaCO3_NH2_100mM/ (time points: 2, 3, 5, 6) │ ├── Aug_CaCO3_NH2_100mM_4_tomo_2 │ ├── Aug_CaCO3_NH2_100mM_4_tomo_3 │ ├── Aug_CaCO3_NH2_100mM_4_tomo_5 │ └── Aug_CaCO3_NH2_100mM_4_tomo_6 │ └── CaCO3_NH2_50mM/ (time points: 3, 5, 8) ├── Aug_CaCO3_NH2_50mM_1_tomo_3 ├── Aug_CaCO3_NH2_50mM_1_tomo_5 ├── Aug_CaCO3_NH2_50mM_1_tomo_8 └── Aug_CaCO3_NH2_50mM_1_tomo_10 5. METHODS ---------- X-ray micro-computed tomograms were acquired from ID11, European Synchrotron Radiation Facility (ESRF), Grenoble, FR. Measurements were carried out using a focused beam at ~32 keV. Projections were collected using a FReLoN4m detector with high resolution. 1024 projections were acquired for each tomography between 0–180 degrees at 0.15 seconds exposure. The resulting 3D volumes had a voxel size of 1.2 μm. X-ray diffraction computed tomograms wree acquired from at ID11 at the ESRF, using a 30 × 30 μm parallel beam with wavelength λ = 0.038697 nm. The energy was chosen such that the Q range of calcium carbonate polymorphs is covered. The beam was focused to a μm size and diffraction patterns were collected using a Dectris Eiger2 X CdTe 4M detector. The detector was calibrated using CeO2 NIST standard. The sample – calcium carbonate embedded in controlled pore glass rods (CPG) - was mounted on a stage with movements in x, y, z axes. During each XDR-CT measurement, 61 translational steps across y axis with 90 °angular steps of 2° in the range of 180° were collected, generating a total of 5490 2D diffraction patterns. The exposure time for each scan is 0.59 s. The XRD-CT data obtained from ID11, ESRF was analysed by azimuthally integrating each 2D diffraction frame using PyFAI. This converts the 2D diffraction pattern recorded at every scan position into a 1D diffraction profile. A trimmed mean filter (20%) was used to remove the artefacts arising from hot spots. The background was then subtracted by subtracting the control from the sample diffraction profile. Local diffraction fitting was made using peak-fitting methods in a software XRDUA, which yields phase composition. Finally, the fitted parameters are mapped spatially to reveal the distribution of polymorphs (calcite, vaterite and aragonite). RGB correction of data sets was done using ImageJ.