Smooth 2D manifold extraction from 3D image stack

Research output: Research - peer-reviewJournal article – Annual report year: 2017

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  • Author: Shihavuddin, Asm

    PSL Research University

  • Author: Basu, Sreetama

    PSL Research University

  • Author: Rexhepaj, Elton

    PSL Research University

  • Author: Delestro, Felipe

    CNRS

  • Author: Menezes, Nikita

    CNRS

  • Author: Sigoillot, Séverine M.

    PSL Research University

  • Author: Del Nery, Elaine

    PSL Research University

  • Author: Selimi, Fekrije

    PSL Research University

  • Author: Spassky, Nathalie

    CNRS

  • Author: Genovesio, Auguste

    CNRS

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Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy.

Original languageEnglish
Article number15638
JournalNature Communications
Volume8
ISSN2041-1723
DOIs
StatePublished - 31 May 2017
Externally publishedYes
CitationsWeb of Science® Times Cited: 3
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