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

Cárdenes, Rubén; Zhang, Chong; Klementieva, Oxana LU ; Werner, Stephan; Guttmann, Peter; Pratsch, Christoph; Cladera, Josep and Bijnens, Bart H. (2017) In PLoS ONE 12(4).
Abstract

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... (More)

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.

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publication status
published
subject
in
PLoS ONE
volume
12
issue
4
publisher
Public Library of Science
external identifiers
  • scopus:85017098597
  • wos:000399352000006
ISSN
1932-6203
DOI
10.1371/journal.pone.0174324
language
English
LU publication?
yes
id
55131fdb-71f8-4187-8ad9-7c3d00211eff
date added to LUP
2017-05-23 11:02:52
date last changed
2017-09-18 11:36:53
@article{55131fdb-71f8-4187-8ad9-7c3d00211eff,
  abstract     = {<p>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.</p>},
  articleno    = {e0174324},
  author       = {Cárdenes, Rubén and Zhang, Chong and Klementieva, Oxana and Werner, Stephan and Guttmann, Peter and Pratsch, Christoph and Cladera, Josep and Bijnens, Bart H.},
  issn         = {1932-6203},
  language     = {eng},
  month        = {04},
  number       = {4},
  publisher    = {Public Library of Science},
  series       = {PLoS ONE},
  title        = {3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy : A pilot study},
  url          = {http://dx.doi.org/10.1371/journal.pone.0174324},
  volume       = {12},
  year         = {2017},
}