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Author Gatica, M.; Navarro, C.F.; Lavado, A.; Reig, G.; Pulgar, E.; Llanos, P.; Haertel, S.; Ravasio, A.; Bertocchi, C.; Concha, M.L.; Cerda, M.
Title VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks Type
Year 2023 Publication BMC Bioinformatics Abbreviated Journal BMC Bioinformatics
Volume 24 Issue 1 Pages 283
Keywords Microscopy; Image processing; 3D projections; Virtual 3D peeling
Abstract Motivation Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrates, invertebrates and plants, such as zebrafish, killifish, Drosophila or Marchantia, mainly comprise multilayer tissues, and even if microscopes can reach the needed depth, their geometry hinders the selection and subsequent analysis of the optical volumes of interest. Computational tools to “peel” tissues by removing specific layers and reducing 3D volume into planar images, can critically improve visualization and analysis.Results We developed VolumePeeler, a versatile FIJI plugin for virtual 3D “peeling” of image stacks. The plugin implements spherical and spline surface projections. We applied VolumePeeler to perform peeling in 3D images of spherical embryos, as well as non-spherical tissue layers. The produced images improve the 3D volume visualization and enable analysis and quantification of geometrically challenging microscopy datasets.
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1471-2105 ISBN Medium
Area Expedition Conference
Notes WOS:001029240200002 Approved
Call Number UAI @ alexi.delcanto @ Serial 1853
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