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LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation

Sarah Machado, Vincent Mercier, View ORCID ProfileNicolas Chiaruttini
doi: https://doi.org/10.1101/267534
Sarah Machado
1Marcos González Gaitán lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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Vincent Mercier
2Aurélien Roux lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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Nicolas Chiaruttini
2Aurélien Roux lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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  • ORCID record for Nicolas Chiaruttini
  • For correspondence: nicolas.chiaruttini@unige.ch
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Abstract

Bioimage analysis is an important preliminary step required for data representation and quantitative studies. To carry out these tasks, we developed LimeSeg, an easy-to-use, efficient and modular 3D image segmentation method. Based on the idea of SURFace ELements, LimeSeg resembles a highly coarse-grained simulation of a lipid membrane in which a set of particles, analogous to lipid molecules, are attracted to local image maxima. The particles are self-generating and self-destructing thus providing the ability for the membrane to evolve towards the contour of the object of interest. We characterize the emergent mechanical properties of this system and show how it can be used to segment many 3D objects from numerous types of image of biological samples (brain MRI, cell epithelium, cellular organelles). LimeSeg is available as a Fiji plugin that includes simple commands, a 3D visualizer, and customization options via ImageJ scripting.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 18, 2018.
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LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation
Sarah Machado, Vincent Mercier, Nicolas Chiaruttini
bioRxiv 267534; doi: https://doi.org/10.1101/267534
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LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation
Sarah Machado, Vincent Mercier, Nicolas Chiaruttini
bioRxiv 267534; doi: https://doi.org/10.1101/267534

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