Research Data Leeds Repository

Citation

Jiang, Zhao, Gao, Zirui, Appel, Christian, Durelle, Maxime, Turner, Thomas, Menzel, Andreas, Kulak, Alexander N., Kim, Yi-Yeoun, Guizar-Sicairos, Manuel, Holler, Mirko, Meldrum, Fiona C. and Ihli, Johannes (2026) Data for 'In Situ Ptychographic X-ray Nanotomography of Temperature-Controlled Crystallization Processes'. University of Leeds. [Dataset] https://doi.org/10.5518/1842

Dataset description

This dataset contains X-ray computed tomograms and derived data acquired during in situ ptychographic X-ray nanotomography experiments investigating temperature-controlled crystallization processes. Data were collected at the cSAXS beamline at the Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Villigen, Switzerland, in March 2023. The dataset comprises two sets of three-dimensional tomographic reconstructions: eight tomograms reconstructed via filtered back projection (following registration and masking), and 80 tomograms derived from dynamic reconstruction (masked). Additional derived data includes electron density histograms, sub-tomograms obtained following principal component analysis (PCA) and clustering, and time-resolved temperature measurements recorded throughout the experiments. The dataset is accompanied by a suite of MATLAB scripts supporting: automated masking of 80 tomograms, PCA analysis, electron density histogram extraction, and crystallization likelihood extraction.

Subjects:	F000 - Physical sciences > F100 - Chemistry > F130 - Structural chemistry > F131 - Crystallography
Divisions:	Faculty of Engineering and Physical Sciences > School of Chemistry
Date deposited:	17 Apr 2026 20:06
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/1539
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Jiang, Zhao https://orcid.org/0009-0009-0688-5915 University of Leeds https://ror.org/024mrxd33 ror Gao, Zirui https://orcid.org/0000-0003-2498-0122 National Synchrotron Light Source II https://ror.org/01q47ea17 ror Appel, Christian https://orcid.org/0000-0002-6050-3836 Paul Scherrer Insitut https://ror.org/03eh3y714 ror Durelle, Maxime University of Leeds https://ror.org/024mrxd33 ror Turner, Thomas https://orcid.org/0000-0003-3776-2044 University of Leeds https://ror.org/024mrxd33 ror Menzel, Andreas https://orcid.org/0000-0002-0489-609X Paul Scherrer Insitut https://ror.org/03eh3y714 ror Kulak, Alexander N. https://orcid.org/0000-0002-2798-9301 University of Leeds https://ror.org/024mrxd33 ror Kim, Yi-Yeoun https://orcid.org/0000-0002-8503-4554 University of Leeds https://ror.org/024mrxd33 ror Guizar-Sicairos, Manuel https://orcid.org/0000-0002-8293-3634 Paul Scherrer Insitut https://ror.org/03eh3y714 ror Holler, Mirko https://orcid.org/0000-0001-8141-0148 Paul Scherrer Insitut https://ror.org/03eh3y714 ror Meldrum, Fiona C. https://orcid.org/0000-0001-9243-8517 University of Leeds https://ror.org/024mrxd33 ror Ihli, Johannes https://orcid.org/0000-0002-9541-5748 Paul Scherrer Insitut https://ror.org/03eh3y714 ror Type of data: Dataset Research funders: European Research Council, Engineering and Physical Sciences Research Council, China Scholarship Council, Swiss National Science Foundation, EU Horizon 2020 Grant numbers: 788968, EP/R018820/1, 200021_178788 and PZ00P2_179886, PSI-FELLOW-III-3i 884104 Publication date: 2026 Resource language: English Metadata language: English Publisher: University of Leeds Last Modified: 20 Apr 2026 08:27

Files

Documentation

README [10kB] README [10kB] README [10kB] Security: Anyone File name: README_Jiang-etal_2026.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 10kB

mit_licence.txt [1kB] mit_licence.txt [1kB] mit_licence.txt [1kB] Security: Anyone File name: mit_licence.txt Content type: Documentation Mime-Type: text/plain File size: 1kB

Data

Data-Dynamic_tomograms.zip [4GB] Data-Dynamic_tomograms.zip [4GB] Data-Dynamic_tomograms.zip [4GB] Security: Anyone File name: Data-Dynamic_tomograms.zip Content type: Data Description: Each .tif file is a slice of the upsampled tomogram reconstructed using dynamic reconstruction, representing a slice of volume. each .tif stack contains 218 image sequences, each represents a timepoint in total of 218 timepoints. Files are named sequentia Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 4GB

Data-FBP_tomograms [5GB] Data-FBP_tomograms [5GB] Data-FBP_tomograms [5GB] Security: Anyone File name: Data-FBP_tomograms.zip Content type: Data Description: Each .tif file is a tomogram reconstructed using Filtered Back Projection, representing a single timepoint in a time-series dataset. Files are named sequentially from S1 to S8, corresponding to 8 timepoints in total. Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 5GB

Data-Electron_density_histogram.txt [130kB] Data-Electron_density_histogram.txt [130kB] Data-Electron_density_histogram.txt [130kB] Security: Anyone File name: Data-Electron_density_histogram.txt Content type: Data Description: This txt file lists the electron density histogram of all 63 slices in the dynamically reconstructed tomogram. Electron density is filtered from 01-0.9 and distributed in 255 bins. Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 130kB

Data-Scan_number_vs_temperature.xlsx [25kB] Data-Scan_number_vs_temperature.xlsx [25kB] Data-Scan_number_vs_temperature.xlsx [25kB] Security: Anyone File name: Data-Scan_number_vs_temperature.xlsx Content type: Data Description: This xlxs file record the temperature at each scan number. Mime-Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 25kB

Program

Code-4Darray.m [15kB] Code-4Darray.m [15kB] Code-4Darray.m [15kB] Security: Anyone File name: Code-4Darray.m Content type: Program Description: This MATLAB script extracts the electron density of each voxel across all 63 slices of the dynamically reconstructed tomogram (each contains 218 timepoints), and analyses the rate of electron density change over user-selected heating periods (e.g. 40–60°C Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 15kB

Code-Auto_masking_upsampled.m [2kB] Code-Auto_masking_upsampled.m [2kB] Code-Auto_masking_upsampled.m [2kB] Security: Anyone File name: Code-Auto_masking_upsampled.m Content type: Program Description: This MATLAB script automatically segments and masks tomograms by removing background and noise. Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 2kB

Code-Get_histo_analysis.m [1kB] Code-Get_histo_analysis.m [1kB] Code-Get_histo_analysis.m [1kB] Security: Anyone File name: Code-Get_histo_analysis.m Content type: Program Description: This MATLAB script extracts electron density histograms from 63 slices in the dynamically reconstructed tomogram, filtering electron density values within the range of 0.1 to 0.9 and distributing them into 255 bins. Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 1kB

Code-PCA.m [5kB] Code-PCA.m [5kB] Code-PCA.m [5kB] Security: Anyone File name: Code-PCA.m Content type: Program Description: This MATLAB script performs Principal Component Analysis (PCA) on the voxel electron density values across 63 slices in the dynamically reconstructed tomogram. Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 5kB

Code-Rate_analysis_after_PCA.m [18kB] Code-Rate_analysis_after_PCA.m [18kB] Code-Rate_analysis_after_PCA.m [18kB] Security: Anyone File name: Code-Rate_analysis_after_PCA.m Content type: Program Description: This MATLAB script performs rate analysis on 63 tomogram slices reconstructed by dynamic reconstruction after processed by PCA. Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 18kB