Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

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dc.contributor.authorBaybay, Erod Keatonen
dc.contributor.authorEsposito, Ericen
dc.contributor.authorHauf, Silkeen
dc.contributor.departmentBiological Sciencesen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2021-02-02T20:33:21Zen
dc.date.available2021-02-02T20:33:21Zen
dc.date.issued2020-10-06en
dc.description.abstractThree-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regions. The diameter of these spheres adapts to the cell diameter at each position. Thus, Pomegranate accurately represents radially symmetric cells in 3D even if cell diameter varies and regardless of whether a cell is straight, bent or curved. We have tested Pomegranate on fission yeast and demonstrate its ability to 3D segment wild-type cells as well as classical size and shape mutants. The pipeline is available as a macro for the open-source image analysis software Fiji/ImageJ. 2D segmentations created within or outside Pomegranate can serve as input, thus making this a valuable extension to the image analysis portfolio already available for fission yeast and other radially symmetric cell types.en
dc.description.notesResearch reported in this publication was supported by the National Institute of General Medical Sciences (NIGMS) of the National Institute of Health (NIH) under award number R35GM119723 and by the National Science Foundation under Grant no. 1616247.en
dc.description.sponsorshipNational Institute of General Medical Sciences (NIGMS) of the National Institute of Health (NIH) [R35GM119723]; National Science FoundationNational Science Foundation (NSF) [1616247]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41598-020-73597-wen
dc.identifier.issn2045-2322en
dc.identifier.issue1en
dc.identifier.other16580en
dc.identifier.pmid33024177en
dc.identifier.urihttp://hdl.handle.net/10919/102202en
dc.identifier.volume10en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titlePomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cellsen
dc.title.serialScientific Reportsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen
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