title: 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study.
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.
authors.affiliation: Physense, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Rubén
authors.initials: R
authors.lastname: Cárdenes
authors.affiliation: Physense, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Chong
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Institute of Neuropathology, IDIBELL-University Hospital Bellvitge, L'Hospitalet de Llobregat, Spain.|Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden.
authors.forename: Oxana
authors.initials: O
authors.lastname: Klementieva
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Werner
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Guttmann
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Pratsch
authors.affiliation: Biophysics Unit & Centre of Studies in Biophysics, Dept. of Biochemistry & Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Cladera
authors.affiliation: Physense, Universitat Pompeu Fabra, Barcelona, Spain.|ICREA, Barcelona, Spain.
authors.forename: Bart H
authors.identifier: http://orcid.org/0000-0003-3130-6937
authors.initials: BH
authors.lastname: Bijnens
mesh_terms: D000465:Algorithms; D002460:Cell Line; D002462:Cell Membrane / Q000648:ultrastructure*; D015925:Cryopreservation; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods* / Q000706:statistics & numerical data; D008853:Microscopy / Q000379:methods* / Q000706:statistics & numerical data; D019047:Phantoms, Imaging; D010865:Pilot Projects; D012984:Software; D014965:X-Rays