research-article

Simulating Organogenesis: Algorithms for the Image-Based Determination of Displacement Fields

Authors:

Clemens Arthur Schwaninger,

Denis Menshykau,

Dagmar IberAuthors Info & Claims

ACM Transactions on Modeling and Computer Simulation (TOMACS), Volume 25, Issue 2

Article No.: 10, Pages 1 - 19

https://doi.org/10.1145/2688908

Published: 17 February 2015 Publication History

Abstract

Recent advances in imaging technology now provide us with 3D images of developing organs. These can be used to extract 3D geometries for simulations of organ development. To solve models on growing domains, the displacement fields between consecutive image frames need to be determined. Here we develop and evaluate different landmark-free algorithms for the determination of such displacement fields from image data. In particular, we examine minimal distance, normal distance, diffusion-based, and uniform mapping algorithms and test these algorithms with both synthetic and real data in 2D and 3D. We conclude that in most cases, the normal distance algorithm is the method of choice and wherever it fails, diffusion-based mapping provides a good alternative.

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Cited By

Qiu RTsai MChen YSingh SLo C(2024)Integrated Automatic Optical Inspection and Image Processing Procedure for Smart Sensing in Production LinesSensors10.3390/s2405161924:5(1619)Online publication date: 1-Mar-2024
https://doi.org/10.3390/s24051619
Mederacke MConrad LDoumpas NVetter RIber D(2023)Geometric effects position renal vesicles during kidney developmentCell Reports10.1016/j.celrep.2023.11352642:12(113526)Online publication date: Dec-2023
https://doi.org/10.1016/j.celrep.2023.113526
Menshykau DMichos OLang CConrad LMcMahon AIber D(2019)Image-based modeling of kidney branching morphogenesis reveals GDNF-RET based Turing-type mechanism and pattern-modulating WNT11 feedbackNature Communications10.1038/s41467-018-08212-810:1Online publication date: 16-Jan-2019
https://doi.org/10.1038/s41467-018-08212-8
Show More Cited By

Simulating Organogenesis: Algorithms for the Image-Based Determination of Displacement Fields
1. Computing methodologies
  1. Computer graphics
2. Theory of computation

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Published In

cover image ACM Transactions on Modeling and Computer Simulation

ACM Transactions on Modeling and Computer Simulation Volume 25, Issue 2

Special Issue on Computational Methods in Systems Biology

April 2015

161 pages

ISSN:1049-3301

EISSN:1558-1195

DOI:10.1145/2737798

Editor:
Adelinde M. Uhrmacher
University of Rostock, Germany

Issue’s Table of Contents

Copyright © 2015 ACM.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 17 February 2015

Accepted: 01 October 2014

Revised: 01 July 2014

Received: 01 January 2014

Published in TOMACS Volume 25, Issue 2

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SystemsX grants of the Swiss National Fund (SNF)

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Cited By

Qiu RTsai MChen YSingh SLo C(2024)Integrated Automatic Optical Inspection and Image Processing Procedure for Smart Sensing in Production LinesSensors10.3390/s2405161924:5(1619)Online publication date: 1-Mar-2024
https://doi.org/10.3390/s24051619
Mederacke MConrad LDoumpas NVetter RIber D(2023)Geometric effects position renal vesicles during kidney developmentCell Reports10.1016/j.celrep.2023.11352642:12(113526)Online publication date: Dec-2023
https://doi.org/10.1016/j.celrep.2023.113526
Menshykau DMichos OLang CConrad LMcMahon AIber D(2019)Image-based modeling of kidney branching morphogenesis reveals GDNF-RET based Turing-type mechanism and pattern-modulating WNT11 feedbackNature Communications10.1038/s41467-018-08212-810:1Online publication date: 16-Jan-2019
https://doi.org/10.1038/s41467-018-08212-8
Multerer MWittwer LStopka ABarac DLang CIber D(2018)Simulation of Morphogen and Tissue DynamicsMorphogen Gradients10.1007/978-1-4939-8772-6_13(223-250)Online publication date: 16-Oct-2018
https://doi.org/10.1007/978-1-4939-8772-6_13
Iber DKarimaddini ZÜnal E(2015)Image-based modelling of organogenesisBriefings in Bioinformatics10.1093/bib/bbv09317:4(616-627)Online publication date: 27-Oct-2015
https://doi.org/10.1093/bib/bbv093

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