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DEVILS: a tool for the visualization of large datasets with a high dynamic range

The number of grey values that can be displayed on monitors and be processed by the human eye is smaller than the dynamic range of image-based sensors. This makes the visualization of such data a challenge, especially with specimens where small dim structures are equally important as large bright on...

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Autores principales: Guiet, Romain, Burri, Olivier, Chiaruttini, Nicolas, Hagens, Olivier, Seitz, Arne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097733/
https://www.ncbi.nlm.nih.gov/pubmed/33976878
http://dx.doi.org/10.12688/f1000research.25447.2
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author Guiet, Romain
Burri, Olivier
Chiaruttini, Nicolas
Hagens, Olivier
Seitz, Arne
author_facet Guiet, Romain
Burri, Olivier
Chiaruttini, Nicolas
Hagens, Olivier
Seitz, Arne
author_sort Guiet, Romain
collection PubMed
description The number of grey values that can be displayed on monitors and be processed by the human eye is smaller than the dynamic range of image-based sensors. This makes the visualization of such data a challenge, especially with specimens where small dim structures are equally important as large bright ones, or whenever variations in intensity, such as non-homogeneous staining efficiencies or light depth penetration, becomes an issue. While simple intensity display mappings are easily possible, these fail to provide a one-shot observation that can display objects of varying intensities. In order to facilitate the visualization-based analysis of large volumetric datasets, we developed an easy-to-use ImageJ plugin enabling the compressed display of features within several magnitudes of intensities. The Display Enhancement for Visual Inspection of Large Stacks plugin (DEVILS) homogenizes the intensities by using a combination of local and global pixel operations to allow for high and low intensities to be visible simultaneously to the human eye. The plugin is based on a single, intuitively understandable parameter, features a preview mode, and uses parallelization to process multiple image planes. As output, the plugin is capable of producing a BigDataViewer-compatible dataset for fast visualization. We demonstrate the utility of the plugin for large volumetric image data.
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spelling pubmed-80977332021-05-10 DEVILS: a tool for the visualization of large datasets with a high dynamic range Guiet, Romain Burri, Olivier Chiaruttini, Nicolas Hagens, Olivier Seitz, Arne F1000Res Software Tool Article The number of grey values that can be displayed on monitors and be processed by the human eye is smaller than the dynamic range of image-based sensors. This makes the visualization of such data a challenge, especially with specimens where small dim structures are equally important as large bright ones, or whenever variations in intensity, such as non-homogeneous staining efficiencies or light depth penetration, becomes an issue. While simple intensity display mappings are easily possible, these fail to provide a one-shot observation that can display objects of varying intensities. In order to facilitate the visualization-based analysis of large volumetric datasets, we developed an easy-to-use ImageJ plugin enabling the compressed display of features within several magnitudes of intensities. The Display Enhancement for Visual Inspection of Large Stacks plugin (DEVILS) homogenizes the intensities by using a combination of local and global pixel operations to allow for high and low intensities to be visible simultaneously to the human eye. The plugin is based on a single, intuitively understandable parameter, features a preview mode, and uses parallelization to process multiple image planes. As output, the plugin is capable of producing a BigDataViewer-compatible dataset for fast visualization. We demonstrate the utility of the plugin for large volumetric image data. F1000 Research Limited 2021-03-22 /pmc/articles/PMC8097733/ /pubmed/33976878 http://dx.doi.org/10.12688/f1000research.25447.2 Text en Copyright: © 2021 Guiet R et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Guiet, Romain
Burri, Olivier
Chiaruttini, Nicolas
Hagens, Olivier
Seitz, Arne
DEVILS: a tool for the visualization of large datasets with a high dynamic range
title DEVILS: a tool for the visualization of large datasets with a high dynamic range
title_full DEVILS: a tool for the visualization of large datasets with a high dynamic range
title_fullStr DEVILS: a tool for the visualization of large datasets with a high dynamic range
title_full_unstemmed DEVILS: a tool for the visualization of large datasets with a high dynamic range
title_short DEVILS: a tool for the visualization of large datasets with a high dynamic range
title_sort devils: a tool for the visualization of large datasets with a high dynamic range
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097733/
https://www.ncbi.nlm.nih.gov/pubmed/33976878
http://dx.doi.org/10.12688/f1000research.25447.2
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