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3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: a pilot study

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dc.contributor.author Cardenes, Rubén
dc.contributor.author Zhang, Chong
dc.contributor.author Klementieva, Oxana
dc.contributor.author Werner, Stephan
dc.contributor.author Guttmann, Peter
dc.contributor.author Pratsch, Christoph
dc.contributor.author Cladera i Cerdà, Josep
dc.contributor.author Bijnens, Bart
dc.date.accessioned 2018-02-13T11:51:32Z
dc.date.available 2018-02-13T11:51:32Z
dc.date.issued 2017
dc.identifier.citation Cárdenes R, Zhang C, Klementieva O, Werner S, Guttmann P, Pratsch C, Cladera J, Bijnens BH. 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: a pilot study. PLoS ONE. 2017; 12(4): e0174324. DOI: 10.1371/journal.pone.0174324
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10230/33846
dc.description.abstract Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis.
dc.description.sponsorship R.C. was partially funded by the Instituto de Salud Carlos III, Spain (FIS- PI11/01709), and BE-DGR 2012 BE1 00308 from AGAUR, Catalonia, Spain. C.Z. acknowledges the financial support from the Spanish Ministry of Economy and Competitiveness, through the Maria de Maeztu Programme for Centres/Units of Excellence in R&D (MDM-2015-0502). O.K. was supported by the Seventh Framework Program of the European Commission, grant agreement 278486: DEVELAGE. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under BioStruct-X (grant agreement N283570), the Spanish Ministry of Economy and Competitiveness (grant TIN2014-52923-R) and FEDER.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.relation.ispartof 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: a pilot study. PLoS ONE. 2017; 12(4): e0174324.
dc.rights © 2017 Cárdenes et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Citologia
dc.title 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: a pilot study
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0174324
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/278486
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/283570
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/TIN2014-52923-R
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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