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Smooth 2D manifold extraction from 3D image stack

Author

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  • Asm Shihavuddin

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University)

  • Sreetama Basu

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University
    Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, PSL Research University)

  • Elton Rexhepaj

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University
    Biophenics, Departement de Recherche Translationnelle, Institut Curie, PSL Research University)

  • Felipe Delestro

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University)

  • Nikita Menezes

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University)

  • Séverine M Sigoillot

    (Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, PSL Research University)

  • Elaine Del Nery

    (Biophenics, Departement de Recherche Translationnelle, Institut Curie, PSL Research University)

  • Fekrije Selimi

    (Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, PSL Research University)

  • Nathalie Spassky

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University)

  • Auguste Genovesio

    (Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, PSL Research University)

Abstract

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.

Suggested Citation

  • Asm Shihavuddin & Sreetama Basu & Elton Rexhepaj & Felipe Delestro & Nikita Menezes & Séverine M Sigoillot & Elaine Del Nery & Fekrije Selimi & Nathalie Spassky & Auguste Genovesio, 2017. "Smooth 2D manifold extraction from 3D image stack," Nature Communications, Nature, vol. 8(1), pages 1-8, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15554
    DOI: 10.1038/ncomms15554
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