Data underlying Chapter 5 “Dynamic Bidirectional Coupling of Membrane Morphology and Rod Organization in Flexible Vesicles”, in the PhD thesis: Particle–Membrane Interactions in Biomimetic Vesicles : From Engulfment to Flexible Confinement

This dataset belongs to Chapter 5 of the PhD thesis of Stijn van der Ham (2026). Authors: Stijn van der Ham, Hanumantha Rao Vutukuri Active Soft Matter and Bio-inspired Materials Lab, Faculty of Science and Technology, MESA+ Institute, University of Twente, Enschede, The Netherlands Corresponding Author: Hanumantha Rao Vutukuri (email: h.r.vutukuri@utwente.nl) ***General Introduction*** The dataset contains the experimental data, analysis, and figure files underlying the figures in Chapter 5 of the PhD thesis of Stijn van der Ham. This chapter has been published as: Dynamic bidirectional coupling of membrane morphology and rod organization in flexible vesicles (https://doi.org/10.1073/pnas.2604848123) ***Methodology*** All data processing and analysis steps are described in detail in the Methods section of the corresponding chapter in the thesis. Analysis codes in the dataset can be run as is, with the exception of updating certain paths/parameters as indicated in the analysis codes. ***Organization of the dataset*** The data is organized per figure, numbered according to the thesis, with supporting figures preceded by the capital letter 'S'. Within each figure folder, data is ordered as: - Figure files: final figure files, provided in several formats (.ai file, .pdf file, .svg file) - Raw data folder: raw data underlying the figure (simulation snapshots and microscopy images in the form of .tiff images/stacks/series and .png files) - Analysis folder: analysis codes underlying the figure, data required for the analyses code, and codes for the generation of the plots (jupyter notebooks, .svg files for generated figures.)