Published August 6, 2024 | Version v1
Dataset Open

Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models

Authors/Creators

  • 1. ROR icon Leiden University

Description

Microscopy time-lapses and simulation data needed to reproduce the results from the manuscript “Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models”
by T.M. Vergroesen, V. Vermeulen and R.M.H. Merks

  • "Figure 1":  This folder contains phase contrast time-lapses of endothelial network formation in subfolder "Data" and the image analysis output in subfolder "Output" which can be used to generate results of figure 1 of the paper
  • "Figure 2": This folder contains all simulation data in subfolder "Data" and the image analysis output in subfolder "Output" which can be used to generate results of figure 2 of the paper
  • "Figure 3":  This folder contains phase contrast time-lapsesin subfolder "Data" and the image analysis output in subfolder "Output" which can be used to generate results of figure 3 of the paper
  • "Figure 4": This folder contains all simulation data in subfolder "Data" and the image analysis output in subfolder "Output" which can be used to generate results of figure 4 of the paper

Files

Data for Manuscript.zip

Files (89.2 GB)

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md5:953b0f3fa327fa234d464f729867eb34
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Additional details

Related works

Is part of
Preprint: 10.1101/2024.08.06.606790 (DOI)

Funding

Dutch Research Council
Mathematics-based strategies for repairing tumour blood vessels 865.17.004

Software

Repository URL
https://github.com/mathbioleiden/Tissue-Simulation-Toolkit
Programming language
C++ , Python
Development Status
Active

References

  • Merks RMH, Brodsky SV, Goligorksy MS, Newman SA, Glazier JA. Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Dev Biol. 2006 Jan 1;289(1):44–54.
  • Merks RMH, Perryn ED, Shirinifard A, Glazier JA. Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth. PLOS Comput Biol. 2008 Sep 19;4(9):e1000163.
  • van Oers RFM, Rens EG, LaValley DJ, Reinhart-King CA, Merks RMH. Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro. PLOS Comput Biol. 2014 Aug;10(8):1–14.