Project Title: Lagrangian µ-Particle Tracking Velocimetry Analysis of Microscale Flow over Structured Surfaces - Project: SFB1615 - Subproject: A04 - Self-regulating enhanced surfaces for autonomously operated bioprocesses - Project: SFB1615 - Subproject: A06 - Development of novel, highly active, and selective multifunctional carbon nanotube-supported catalysts for the chemical hydrogenolysis of glycerol to 1,2 propanediol - Project: SFB1615 - Subproject: B04 - Tailored transport processes in multiphase reactors Related Publication: 10.1021/acs.iecr.6c01159 Authors: Timo Merbach (https://orcid.org/0000-0002-7723-5444) (Institute of Multiphase Flows, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany) Jan H. Nissen (https://orcid.org/0009-0004-2915-6890) (Heinrich-Blasius-Institute, Hamburg University of Applied Sciences, Berliner Tor 21, Hamburg 20099, Germany) Fabian Riebesehl (https://orcid.org/0009-0003-2611-7688) (Institute of Polymers and Composites, Hamburg University of Technology, Denickestraße 15, Hamburg 21073, Germany) Lukas Rennpferdt (https://orcid.org/0000-0003-2938-694X) (Institute of Microsystems Technology, Hamburg University of Technology, Eißendorfer Straße 42, Hamburg 21073, Germany) Eike Steuwe (https://orcid.org/0009-0001-7213-7159) (Heinrich-Blasius-Institute, Hamburg University of Applied Sciences, Berliner Tor 21, Hamburg 20099, Germany) Marko Hoffmann (Institute of Multiphase Flows, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany) Alexandra von Kameke (https://orcid.org/0000-0002-1913-774X) (Heinrich-Blasius-Institute, Hamburg University of Applied Sciences, Berliner Tor 21, Hamburg 20099, Germany) Funding Acknowledgement: This dataset was generated as part of the DFG-funded project CRC 1615: SMART Reactors for Future Process Engineering (DFG Project Number: 503850735). ________________________________________ 1. General Information Dataset Title: Data supplement for publication: Lagrangian µ-Particle Tracking Velocimetry Analysis of Microscale Flow over Structured Surfaces Short Description: The TUHH Open Research (TORE) repository contains the raw and processed data underlying the publication "Lagrangian µ-Particle Tracking Velocimetry Analysis of Microscale Flow over Structured Surfaces". The dataset includes experimental particle tracking velocimetry (PTV) data, the design files of the investigated structured surfaces, and the corresponding MATLAB analysis scripts. The study investigates flow over micro- and nanostructured surfaces as a basis for improving (bio)reactor design, with a focus on mass transport near the surface. µ-PTV was used to obtain three-dimensional, time-resolved particle trajectories and velocity fields in a microreactor. The Lagrangian analysis shows that rectangular microgrooves increase particle contact with the wall. In particular, when the microgrooves are oriented perpendicular to the flow. The analysis reveals near-surface phenomena such as particle trapping and localized recirculation that are not captured by averaged Eulerian velocities alone. The dataset is accompanied by this ReadMe file and a separate folder structure file, which describe the file organization, the naming conventions used throughout the repository, and how the individual files relate to the results reported in the associated publication. Date of Data Collection: [2025 – 2026] Geographical Coverage: Germany Keywords: Particle Tracking Velocimetry, Microstructure, Lagrangian analysis, Mass transfer phenomena, Fluid dynamics ________________________________________ 2. Methodological Information Data Collection and Processing Design: The structured surfaces are designed using Inventor Professional 2024 (Autodesk, USA), a computer-aided design software for geometric design. The .stl files of the geometries are generated within Inventor Professional and are included for each geometry case in the main folder. -> Date of creation of the data and author: 05/2025; Timo Merbach Manufacturing of nonporous surfaces: The structures are manufactured using a 3D printer from LightFab (LightFab GmbH, Germany) and fused-silica plates. In a first step, the fused-silica bulk material is locally modified via multi-photon absorption using a highly focused femtosecond laser. In a second step, the modified regions are etched using potassium hydroxide. Manufacturing was carried out at the Institute of Microsystems Technology, Hamburg University of Technology, Eißendorfer Straße 42, 21073 Hamburg, Germany. -> Date of creation of the data and author: 05/2025 to 02/2026; Lukas Rennpferdt Manufacturing of porous surfaces: The nonporous fused-silica plates are made porous using multi-walled carbon nanotube forests. The forest is synthesized on the substrates via a chemical vapor deposition process. Manufacturing was carried out at the Institute of Polymers and Composites, Hamburg University of Technology, Denickestraße 15, 21073 Hamburg, Germany. -> Date of creation of the data and author: 05/2025 to 02/2026; Fabian Riebesehl Experimental: Experimental raw data (image data) are acquired using DaVis 11.2. The images are further processed via volume self-calibration and a Shake-The-Box analysis. Data collection was performed at the Heinrich-Blasius-Institute, Hamburg University of Applied Sciences, Berliner Tor 21, 20099 Hamburg, Germany. -> Date of creation of the data and author: 05/2025 to 02/2026; Timo Merbach, Jan Nissen, Alexandra von Kameke The raw camera/volume data are large and stored on external hard drives. They are not included in this repository but can be made available by the corresponding authors upon reasonable request. The resulting particle trajectories from the Shake-The-Box analysis are exported as .dat files and are included in this repository within the corresponding geometry case folder. The analysis of the trajectories is further described in the analysis procedure below. -> Validation of the experimental setup and analysis procedure: A measurement was conducted using a reference plate with known boundary conditions. The raw data (trajectories), geometry data, and processed data are stored in the Reference_plate folder. -> Lagrangian velocities: The flow field is analyzed in terms of Lagrangian velocities using MATLAB R2024a. The Lagrangian data forms the basis for both the Lagrangian and the Eulerian analysis. The basis for these calculations are the .dat files for each geometry case. Visualization of the flow and computation of Lagrangian quantities are performed in MATLAB R2024a. The trajectory data (.dat), geometry data (.stl, .mat), scripts (.m), and processed data (.mat) are saved in a separate folder for each geometry case. The processed Lagrangian data are located specifically within the Lagrangian subfolder of each case folder. -> Date of creation of the data and author: 05/2025 – 07/2026; Timo Merbach, Jan Nissen, Eike Steuwe, Alexandra von Kameke -> Eulerian flow field: The flow field is analyzed in terms of Eulerian velocity fields using MATLAB R2024a. The Lagrangian data form the basis for the Eulerian analysis. The basis for these calculations are the .dat files for each geometry case. Visualization of the flow and computation of the Eulerian flow field are performed in MATLAB R2024a. The trajectory data (.dat), geometry data (.stl, .mat), scripts (.m), and processed data (.mat) are saved in a separate folder for each geometry case. The processed Eulerian data are located specifically within the Eulerian subfolder of each case folder. -> Date of creation of the data and author: 05/2025 – 07/2026; Timo Merbach, Jan Nissen, Eike Steuwe, Alexandra von Kameke Analysis Procedure The analysis procedure is performed partly using DaVis and partly using MATLAB. First, the raw data recorded with DaVis was calibrated using a volume self-calibration. The data was then preprocessed by subtracting an average image in DaVis to remove stuck particles, followed by a Shake-The-Box analysis, also performed in DaVis. The original camera/volume data are large and stored on external hard drives. They can be made available by the corresponding authors upon reasonable request. The trajectory data from DaVis are exported in .dat format and further analyzed in MATLAB. The MATLAB procedure, including the analysis scripts, geometry files, and processed data files, is provided in the experimental folder. The detailed analysis procedure is described in Section 5. Data collection was performed at the Heinrich-Blasius-Institute, Hamburg University of Applied Sciences, Berliner Tor 21, 20099 Hamburg, Germany. -> Date of creation of the data and author: 05/2025 – 07/2026; Timo Merbach, Jan Nissen, Eike Steuwe, Alexandra von Kameke Experimental design: The experimental setup comprises a syringe pump (KD Scientific Inc., USA), a custom-designed microreactor (microfluidic ChipShop, Germany), and the MUST system (mobile multi-analysis unit for flow investigations in the context of power-to-x technologies and hydrogen applications) at Hamburg University of Applied Sciences. The working fluid is deionized water seeded with fluorescently labeled polystyrene particles. The flow rate is 0.08 mL/min. Experimental measurements are conducted using micro-resolution particle tracking velocimetry (µ-PTV) to analyze the flow field of different structured surfaces within the microreactor. Data Validation and Quality Assurance Data accuracy, completeness, and consistency were ensured through a combination of experimental validation, physical plausibility checks, and comparison with literature values. In particular, fluid-dynamic consistency was evaluated by measuring a reference plate with known boundary conditions and analyzing the reconstructed flow. ________________________________________ 3. Data and File Overview Data are grouped into three case-specific folders corresponding to the investigated surface geometries (Reference_plate, Structured_plate_with_parallel_microgrooves, and Structured_plate_with_perpendicular_microgrooves). Each case folder contains the raw trajectory data (Raw_data) as well as processed data (Processed_data), which is further split into Lagrangian trajectory data (all cases) and, for the Reference_plate and Structured_plate_with_parallel_microgrooves cases, additional Eulerian velocity field data and the underlying scattered interpolants. The corresponding geometry data are saved within each case folder. In addition, it includes this ReadMe file and a separate file describing the overall folder structure (Folder_structure.pdf). Scripts required for the analysis are included in the Folder (Scripts). List of Files and Structure: Folder Description Format Size Reference_plate/ Raw, processed data and scripts Various 2.6 GB Structured_plate_with_parallel_microgrooves/ Raw, processed data and scripts Various 6.8 GB Structured_plate_with_perpendicular_microgrooves/ Raw, processed data and scripts Various 6.3 GB Scripts General scripts .m 16 KB File Naming Conventions The file naming conventions for the structures are as follows: - Reference_plate: Reference plate as a (nonporous) fused-silica plate - Structured_plate_with_parallel_microgrooves: Structured plate with parallel microgrooves and (porous) hydrophilic MWCNTs - Structured_plate_with_perpendicular_microgrooves: Structured plate with perpendicular microgrooves as a (nonporous) fused-silica plate Geometry files File names follow a structured convention, e.g. for the geometry files: 20260702_CRC1615_B04_Reference_plate.stl -> 20260702 = file creation date -> CRC1615 = research project -> B04 = project number -> Reference_plate = description of the structure -> .stl = file format Additional .mat geometry files for visualization of Eulerian velocity fields - mask = geometric mask for the analysis - contour = contour of the microreactor Additional .mat geometry files for statistical analysis - _contour_statistics = contour of the microreactor used for the statistical analysis of trajectories - _mask_statistics = geometric mask used for the visualization within the statistical section PTV Files File names follow a structured convention, e.g. for the PTV files: 20260702_CRC1615_B04_Reference_plate.dat -> 20260702 = file creation date -> CRC1615 = research project -> B04 = project number -> Reference_plate = description of the structure -> .dat = file format Additional identifiers for processed data All result files carry a .mat file extension. The files are categorized into three groups within the folder structure: - Lagrangian folder: processed trajectories - Scattered_Interpolants folder: scattered interpolant data saved for each time step - Eulerian folder: final time-averaged Eulerian velocity fields Lagrangian Files File names follow a structured convention, e.g. for the Lagrangian files: 20260702_CRC1615_B04_Reference_plate_raw_tracks.mat -> 20260702 = file creation date -> CRC1615 = research project -> B04 = project number -> Reference_plate = description of the structure -> raw_tracks = raw imported data after the Shake-The-Box analysis -> .mat = file format Further identifiers used in place of "raw_tracks": - smoothed_tracks = smoothed tracks after Gaussian smoothing - reconnected_filtered_tracks = reconnected and filtered trajectories - statistics = statistics on close surface contact - height_deviation = height deviation calculated along each trajectory Eulerian analysis files File names follow a structured convention, e.g. for the scatteredInterpolant files: Scattered_Interpolants_t_0001.mat -> Scattered_Interpolants = description of the interpolant data -> t_0001 = time step 1 -> .mat = file format File names follow a structured convention, e.g. for the Eulerian files: 20260702_CRC1615_B04_Reference_plate_std.mat -> 20260702 = file creation date -> CRC1615 = research project -> B04 = project number -> Reference_plate = description of the structure -> stddata / veldata = standard error of the velocity data (std) or velocity data (veldata) -> .mat = file format Number of Cases Three different structures were analyzed experimentally: the reference plate, the structured plate with parallel microgrooves, and the structured plate with perpendicular microgrooves. ________________________________________ 4. Access and Licensing Information Repository and Persistent Identifier: Published via TORE, DOI: https://doi.org/10.15480/882.16568 License for Use: CC BY 4.0 Access Restrictions: Open ________________________________________ 5. Reproducibility, Software Dependencies, and Workflow of Analysis Software Requirements - DaVis 11.2 - MATLAB R2024a (including required scripts and workflow files) Data Structure Each PTV case is contained in its own folder, named after the case. Functions required for the analysis are located in the Analysis folder. Analysis File The main analysis script for each case is stored as a .m file in the corresponding case folder. Geometry Files Each case folder contains information related to the reactor design: - An .stl file describing the geometry of the microreactor, including the surface geometry of the region of interest. This file is required for visualizing particle trajectories and forms the basis for calculating the Eulerian velocity fields. - _mask.mat and _contour.mat files, used for visualizing the Eulerian velocity fields. - For the case Structured_plate_with_parallel_microgrooves, additional _mask_statistics.mat and _contour_statistics.mat files are provided for the statistical analysis. Workflow Lagrangian Analysis The Lagrangian analysis is performed for all cases and proceeds as follows: 1. Import and preprocessing: PTV data are imported and relevant parameters are calculated. The resulting data are saved as _raw_tracks.mat in the Processed_data/Lagrangian folder. 2. Trajectory smoothing: Trajectories are smoothed using a Gaussian smoothing filter and saved as _smoothed_tracks.mat in the Processed_data/Lagrangian folder. 3. Particle velocities are computed from the smoothed trajectories via finite-difference differentiation of position with respect to time. An outlier removal is performed for each trajectory point, and trajectories exceeding a defined standard-deviation factor are removed. The filtered trajectories are saved as _reconnected_filtered_tracks.mat. 4. Reactive-region classification: To determine whether a track passes through the reactive region near the structured plate, the contour of the structured plate is buffered outward by 300 micrometers. Each trajectory point is then flagged as inside or outside this buffered (reactive) region, and each track is classified according to whether it starts and/or ends inside or outside this region. The classification results are saved as _statistics.mat. 5. Height deviation: For the Lagrangian analysis, the height deviation of each track relative to its own starting height is computed over time and saved as _height_deviation.mat. Required functions: calculate_std_factor.m, import_dat.m, rotate_track_coords.m, velocities_from_particle_tracks.m Eulerian Analysis Based on the _reconnected_filtered_tracks.mat files, an additional Eulerian analysis is performed for the cases Reference_plate and Structured_plate_with_parallel_microgrooves. 1. The function str_stl.m sets zero velocity at the outer boundaries of the microreactor. 2. Scattered interpolants are computed from the trajectory data for each time step and saved in the Scattered_Interpolants folder. 3. The scattered interpolants are binned onto a regular grid to obtain mean velocities and the standard errors of the velocity, saved as _veldata and _std. Required functions: binningnsave_interp_noexp.m, str_stl.m, inpolyhedron.m str_stl.m: Uses inpolyhedron for point-in-polyhedron testing: Sven (2025). inpolyhedron - are points inside a triangulated volume? (https://de.mathworks.com/matlabcentral/fileexchange/37856-inpolyhedron-are-points-inside-a-triangulated-volume), MATLAB Central File Exchange. Retrieved 2025-11-17. o Running a Case All analyses were performed using MATLAB R2024a. It is therefore recommended to run the analyses with this version to ensure reproducibility. Each geometry case should be run from the main script's folder location, so that all script references resolve correctly. Reproducibility Notes: All processed data and analysis files required to reproduce the reported analysis are included in the dataset, comprising flow measurements and geometry files. All analyses follow standard fluid dynamics principles. ________________________________________ 6. Ethical and Legal Aspects Data Protection: Not applicable, as the dataset does not contain any personal or sensitive data. Consent Statement: Not applicable, as no human participants or personal data are involved. ________________________________________ 7. Versioning and Updates Version Number: v1.0 Date of Release: [2026-09-17] ________________________________________ 8. Contact Information Corresponding Author: Name: Timo Merbach Institution: Institute of Multiphase Flows, Hamburg University of Technology Email: timo.merbach@tuhh.de ORCID: 0000-0002-7723-5444 Project Website: https://www.tuhh.de/sfb1615/welcome