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 and Auguste Genovesio ()
Additional contact information
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

Nature Communications, 2017, vol. 8, issue 1, 1-8

Abstract: 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.

Date: 2017
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/ncomms15554 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15554

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms15554

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().