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  4. NRStitcher: non-rigid stitching of terapixel-scale volumetric images
 
research article

NRStitcher: non-rigid stitching of terapixel-scale volumetric images

Miettinen, Arttu  
•
Oikonomidis, Ioannis Vogiatzis
•
Bonnin, Anne
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December 15, 2019
Bioinformatics

A Summary: In modern microscopy, the field of view is often increased by obtaining an image mosaic, where multiple sub-images are taken side-by-side and combined post-acquisition. Mosaic imaging often leads to long imaging times that can increase the probability of sample deformation during the acquisition due to, e.g. changes in the environment, damage caused by the radiation used to probe the sample or biologically induced deterioration. Here we propose a technique, based on local phase correlation, to detect the deformations and construct an artifact-free image mosaic from deformed sub-images. The implementation of the method supports distributed computing and can be used to generate teravoxel-size mosaics. We demonstrate its capabilities by assembling a 5.6 teravoxel tomographic image mosaic of microvasculature in whole mouse brain. The method is compared to existing rigid stitching implementations designed for very large datasets, and observed to create artifact-free image mosaics in comparable runtime with the same hardware resources.

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Type
research article
DOI
10.1093/bioinformatics/btz423
Web of Science ID

WOS:000509361200027

Author(s)
Miettinen, Arttu  
•
Oikonomidis, Ioannis Vogiatzis
•
Bonnin, Anne
•
Stampanoni, Marco
Date Issued

2019-12-15

Published in
Bioinformatics
Volume

35

Issue

24

Start page

5290

End page

5297

Subjects

Biochemical Research Methods

•

Biotechnology & Applied Microbiology

•

Computer Science, Interdisciplinary Applications

•

Mathematical & Computational Biology

•

Statistics & Probability

•

Biochemistry & Molecular Biology

•

Biotechnology & Applied Microbiology

•

Computer Science

•

Mathematical & Computational Biology

•

Mathematics

•

reconstruction

•

phase

•

CIBM-PC

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
CIBM  
Available on Infoscience
February 8, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/165207
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