VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks

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dc.contributor.authorGatica, Marilyn
dc.contributor.authorNavarro, Carlos F. F.
dc.contributor.authorLavado, Alejandro
dc.contributor.authorReig, German
dc.contributor.authorPulgar, Eduardo
dc.contributor.authorLlanos, Paula
dc.contributor.authorHaertel, Steffen
dc.contributor.authorRavasio, Andrea
dc.contributor.authorBertocchi, Cristina
dc.contributor.authorConcha, Miguel L. L.
dc.contributor.authorCerda, Mauricio
dc.date.accessioned2024-01-10T14:23:25Z
dc.date.available2024-01-10T14:23:25Z
dc.date.issued2023
dc.description.abstractMotivation 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.
dc.fechaingreso.objetodigital2024-05-15
dc.fuente.origenWOS
dc.identifier.doi10.1186/s12859-023-05403-z
dc.identifier.issn1471-2105
dc.identifier.urihttps://doi.org/10.1186/s12859-023-05403-z
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/80094
dc.identifier.wosidWOS:001029240200002
dc.information.autorucFacultad de Ciencias Biológicas; Bertocchi No Informado, Cristina; S/I; 1078032
dc.issue.numero1
dc.language.isoen
dc.nota.accesocontenido completo
dc.publisherBMC
dc.revistaBMC BIOINFORMATICS
dc.rightsacceso abierto
dc.subjectMicroscopy
dc.subjectImage processing
dc.subject3D projections
dc.subjectVirtual 3D peeling
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleVolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks
dc.typeartículo
dc.volumen24
sipa.codpersvinculados1078032
sipa.indexWOS
sipa.trazabilidadCarga SIPA;09-01-2024
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