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*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Original languageEnglish
Article number15638
JournalNature Communications
Volume8
ISSN2041-1723
DOIs
Publication statusPublished - 31 May 2017
Externally publishedYes

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