Smooth 2D manifold extraction from 3D image stack

Asm Shihavuddin; Sreetama Basu; Elton Rexhepaj; Felipe Delestro; Nikita Menezes; Séverine M Sigoillot; Elaine Del Nery; Fekrije Selimi; Nathalie Spassky; Auguste Genovesio

doi:10.1038/ncomms15554

Nature Communications (May 2017)

Smooth 2D manifold extraction from 3D image stack

Asm Shihavuddin,
Sreetama Basu,
Elton Rexhepaj,
Felipe Delestro,
Nikita Menezes,
Séverine M Sigoillot,
Elaine Del Nery,
Fekrije Selimi,
Nathalie Spassky,
Auguste Genovesio

Affiliations

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
Elton Rexhepaj: Institut de Biologie de l’Ecole Normale Superieure (IBENS), CNRS UMR8197, Inserm U1024, Ecole Normale Superieure, 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

DOI: https://doi.org/10.1038/ncomms15554
Journal volume & issue: Vol. 8, no. 1
pp. 1 – 8

Abstract

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Maximum Intensity Projection is a common tool to represent 3D biological imaging data in a 2D space, but it creates artefacts. Here the authors develop Smooth Manifold Extraction, an ImageJ/Fiji plugin, to preserve local spatial relationships when extracting the content of a 3D volume to a 2D space.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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