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  Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions

Scherf, N., Herberg, M., Thierbach, K., Zerjatke, T., Kalkan, T., Humphreys, P., et al. (2012). Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Bioinformatics, 28(18), i556-i561. doi:10.1093/bioinformatics/bts404.

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 Creators:
Scherf, Nico1, Author           
Herberg, M.1, Author
Thierbach, K.1, Author
Zerjatke, T.1, Author
Kalkan, T.1, Author
Humphreys, P.1, Author
Smith, A.1, Author
Glauche, I.1, Author
Roeder, I.1, Author
Affiliations:
1External Organizations, ou_persistent22              

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 Abstract: Motivation: Mouse embryonic stem cells (mESCs) have developed into a prime system to study the regulation of pluripotency in stable cell lines. It is well recognized that different, established protocols for the maintenance of mESC pluripotency support morphologically and functionally different cell cultures. However, it is unclear how characteristic properties of cell colonies develop over time and how they are re-established after cell passage depending on the culture conditions. Furthermore, it appears that cell colonies have an internal structure with respect to cell size, marker expression or biomechanical properties, which is not sufficiently understood. The analysis of these phenotypic properties is essential for a comprehensive understanding of mESC development and ultimately requires a bioinformatics approach to guarantee reproducibility and high-throughput data analysis. Results: We developed an automated image analysis and colony tracking framework to obtain an objective and reproducible quantification of structural properties of cell colonies as they evolve in space and time. In particular, we established a method that quantifies changes in colony shape and (internal) motion using fluid image registration and image segmentation. The methodology also allows to robustly track motion, splitting and merging of colonies over a sequence of images. Our results provide a first quantitative assessment of temporal mESC colony formation and estimates of structural differences between colony growth under different culture conditions. Furthermore, we provide a stream-based visualization of structural features of individual colonies over time for the whole experiment, facilitating visual comprehension of differences between experimental conditions. Thus, the presented method establishes the basis for the model-based analysis of mESC colony development. It can be easily extended to integrate further functional information using fluorescence signals and differentiation markers. Availability: The analysis tool is implemented C++ and Mathematica 8.0 (Wolfram Research Inc., Champaign, IL, USA). The tool is freely available from the authors. We will also provide the source code upon request.

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Language(s): eng - English
 Dates: 2012-09-032012-09-15
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1093/bioinformatics/bts404
PMID: 22962481
PMC: PMC3436831
 Degree: -

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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 28 (18) Sequence Number: - Start / End Page: i556 - i561 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991