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

Rubén Cárdenes, Chong Zhang, Oxana Klementieva, Stephan Werner, Peter Guttmann, Christoph Pratsch, Josep Cladera, Bart H. Bijnens

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)

Abstract

© 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. Structural analysis of biological membranes is important for understanding cell and subcellular 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 subcellular 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.
Original languageEnglish
Article numbere0174324
JournalPLoS ONE
Volume12
Issue number4
DOIs
Publication statusPublished - 1 Apr 2017

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