!!!***** 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 Ptychographic X-ray Nanotomography of Temperature-Controlled Crystallization Processes Creator(s): Zhao Jiang[1], Zirui Gao[2], Christian Appel[3], Maxime Durelle[1], Thomas Turner[1], Andreas Menzel[3], Alexander Kulak[1], Yi-Yeoun Kim[1], Manuel Guizar-Sicairos[3,4], Mirko Holler[3], Fiona Meldrum[1], Johannes Ihli[3] Organisation(s): 1. University of Leeds. 2. Brookhaven National Laboratory, National Synchrotron Light Source II. 3.Paul Scherrer Insitut. 4. École Polytechnique Fédérale de Lausanne. Rights-holder(s):Unless otherwise stated, Copyright 2026 University of Leeds Publication Year: 2026 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. Cite as: Zhao Jiang, Zirui Gao, Christian Appel, Maxime Durelle, Thomas Turner, Andreas Menzel, Alexander Kulak, Yi-Yeoun Kim, Manuel Guizar-Sicairos, Mirko Holler, Fiona Meldrum, Johannes Ihli (2026): In Situ Ptychographic X-ray Nanotomography of Temperature-Controlled Crystallization Processes. University of Leeds. [Dataset] https://doi.org/10.5518/1842 Related publication: Zhao Jiang, Zirui Gao, Christian Appel, Maxime Durelle, Thomas Turner, Andreas Menzel, Alexander Kulak, Yi-Yeoun Kim, Manuel Guizar-Sicairos, Mirko Holler, Fiona Meldrum, Johannes Ihli. In Situ Ptychographic X-ray Nanotomography of Temperature-Controlled Crystallization Processes., Nat. Commun., 2026, Accepted. Contact: violetchiang0621@gmail.com 2. TERMS OF USE --------------- Copyright 2026 University of Leeds, Zhao Jiang, Zirui Gao, Christian Appel, Maxime Durelle, Thomas Turner, Andreas Menzel, Alexander Kulak, Yi-Yeoun Kim, Manuel Guizar-Sicairos, Mirko Holler, Fiona Meldrum, Johannes Ihli. 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: Temporal tomographic synthesis for nanoscale characterization of electrode materials Dates: April 2018 – March 2022 Funding organisation: Swiss National Science Foundation (SNSF) Grant no.: 200021_178788 Title: Resonant Coherent Diffraction Imaging, Towards Quantitative Nanoscopic Correlation Spectrotomography in Heterogeneous Catalysis Dates: January 2019 – April 2022 Funding organisation: Swiss National Science Foundation (SNSF) Grant no.: PZ00P2_179886 Title: PSI-FELLOW-III-3i Dates: 01 September 2020 – 31 August 2025 Funding organisation: European Commission, Horizon 2020 (Marie Skłodowska-Curie COFUND) Grant no.: 884104 Title: Chinese Scholarship Committee Dates: September 2021 – August 2024 Funding organisation: Chinese Scholarship Committee 4. CONTENTS ----------- File listing -Data -Data-Dynamic_tomograms Upsampled_S2_stack_cropped.tif Upsampled_S3_stack_cropped.tif Upsampled_S4_stack_cropped.tif Upsampled_S5_stack_cropped.tif Upsampled_S6_stack_cropped.tif Upsampled_S7_stack_cropped.tif Upsampled_S8_stack_cropped.tif Upsampled_S9_stack_cropped.tif Upsampled_S10_stack_cropped.tif Upsampled_S11_stack_cropped.tif Upsampled_S12_stack_cropped.tif Upsampled_S13_stack_cropped.tif Upsampled_S14_stack_cropped.tif Upsampled_S15_stack_cropped.tif Upsampled_S16_stack_cropped.tif Upsampled_S17_stack_cropped.tif Upsampled_S18_stack_cropped.tif Upsampled_S19_stack_cropped.tif Upsampled_S20_stack_cropped.tif Upsampled_S21_stack_cropped.tif Upsampled_S22_stack_cropped.tif Upsampled_S23_stack_cropped.tif Upsampled_S24_stack_cropped.tif Upsampled_S25_stack_cropped.tif Upsampled_S26_stack_cropped.tif Upsampled_S27_stack_cropped.tif Upsampled_S28_stack_cropped.tif Upsampled_S29_stack_cropped.tif Upsampled_S30_stack_cropped.tif Upsampled_S31_stack_cropped.tif Upsampled_S32_stack_cropped.tif Upsampled_S33_stack_cropped.tif Upsampled_S34_stack_cropped.tif Upsampled_S35_stack_cropped.tif Upsampled_S36_stack_cropped.tif Upsampled_S37_stack_cropped.tif Upsampled_S38_stack_cropped.tif Upsampled_S39_stack_cropped.tif Upsampled_S40_stack_cropped.tif Upsampled_S41_stack_cropped.tif Upsampled_S42_stack_cropped.tif Upsampled_S43_stack_cropped.tif Upsampled_S44_stack_cropped.tif Upsampled_S45_stack_cropped.tif Upsampled_S46_stack_cropped.tif Upsampled_S47_stack_cropped.tif Upsampled_S48_stack_cropped.tif Upsampled_S49_stack_cropped.tif Upsampled_S50_stack_cropped.tif Upsampled_S51_stack_cropped.tif Upsampled_S52_stack_cropped.tif Upsampled_S53_stack_cropped.tif Upsampled_S54_stack_cropped.tif Upsampled_S55_stack_cropped.tif Upsampled_S56_stack_cropped.tif Upsampled_S57_stack_cropped.tif Upsampled_S58_stack_cropped.tif Upsampled_S59_stack_cropped.tif Upsampled_S60_stack_cropped.tif Upsampled_S61_stack_cropped.tif Upsampled_S62_stack_cropped.tif Upsampled_S63_stack_cropped.tif Upsampled_S64_stack_cropped.tif -Data_FBP_tomograms S1_masked.tif S2_masked.tif S3_masked.tif S4_masked.tif S5_masked.tif S6_masked.tif S7_masked.tif S8_masked.tif -Data-Electron_density_histogram.txt -Data-Scan_number_vs_temperature.xlsx -Code -Code-4Darray.m -Code-Auto_masking_upsampled.m -Code-Get_histo_analysis.m -Code-PCA.m -Code-Rate_analysis_after_PCA.m 5. METHODS ---------- Tomogram Acquisition and Reconstruction: Near field ptychographic X-ray computed tomogram experiments were carried out at 6.2 keV at the cSAXS beamline of the Swiss Light Source, Paul Scherrer Institut, Switzerland. The field of view of each projection, or ptychographic scan, was 80 × 45 μm2 (width × height). The sample was scanned using a Fermat-spiral scanning pattern with an average step size of 5 µm and the exposure time per scanning point was 0.05 seconds. For each ptychographic scan, a detector region of 1024 × 1024 pixels was used. The projection pixel size, after binning, was 82.84 nm. Ptychographic reconstructions were performed using the PtychoShelves package with 500 iterations of the difference map algorithm followed by 600 iterations of maximum likelihood refinement. Tomography projection acquisition followed a nested approach, where we acquired 10 equally spaced projections over 180º at a time, and then repeated the acquisition with an angular offset based on the golden ratio. The acquisition scheme was chosen to maximize the angular information diversity for the sparse or dynamic tomogram reconstruction. Following ptychographic image reconstruction and spatial alignment of the projections, tomographic reconstruction was performed using a dynamic sparse reconstruction technique, as first described in Gao et. al (DOI: 10.1126/sciadv.adp3346). The technique allows dynamic tomography reconstruction with increased temporal resolution, which is comparable to the acquisition time of each sparsely sampled tomogram, i.e. each set of 10 projections, and without compromise in spatial resolution. It achieves this by exploiting temporal correlations, under the assumption that the sample evolves only minimally between successive time intervals (set of projections). In practice, a four-dimensional step-function model decomposes the sample dynamics into three constituent tomograms: the initial state, the final state, and a transition-time map. From these three components, one can then reconstruct a full, high-resolution tomogram for each individual time interval, without any a priori structural knowledge of the sample. In comparison to analytic tomographic reconstruction methods, which require approximately 1,250 projections to reconstruct a high-resolution tomogram of an 80 µm sample at 100 nm spatial resolution, the dynamic sparse reconstruction approach applied here achieves comparable image quality using only 10 projections per time point. This represents a >100-fold enhancement in temporal resolution for in-situ measurements, without compromising spatial resolution.