Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields

Sean Robinson 1, 2, * Laurent Guyon 2 Jaakko Nevalainen 1 Mervi Toriseva 1 Malin Akerfelt 1 Matthias Nees 1
* Corresponding author
1 University of Turku
2 BGE - UMR S1038 - Laboratoire de Biologie à Grande Échelle
Abstract : Organotypic, three dimensional (3D) cell culture models of epithelial tumour types such as prostate cancer recapitulate key aspects of the architecture and histology of solid cancers. Morphometric analysis of multicellular 3D organoids is particularly important when additional components such as the extracellular matrix and tumour microenvironment are included in the model. The complexity of such models has so far limited their successful implementation. There is a great need for automatic, accurate and robust image segmentation tools to facilitate the analysis of such biologically relevant 3D cell culture models. We present a segmentation method based on Markov random fields (MRFs) and illustrate our method using 3D stack image data from an organotypic 3D model of prostate cancer cells co-cultured with cancer-associated fibroblasts (CAFs). The 3D segmentation output suggests that these cell types are in physical contact with each other within the model, which has important implications for tumour biology. Segmentation performance is quantified using ground truth labels and we show how each step of our method increases segmentation accuracy. We provide the ground truth labels along with the image data and code. Using independent image data we show that our segmentation method is also more generally applicable to other types of cellular microscopy and not only limited to fluorescence microscopy.
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Journal articles
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https://hal-cea.archives-ouvertes.fr/cea-01820366
Contributor : Marianne Leriche <>
Submitted on : Thursday, June 21, 2018 - 3:26:10 PM
Last modification on : Tuesday, July 16, 2019 - 3:22:42 PM

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Sean Robinson, Laurent Guyon, Jaakko Nevalainen, Mervi Toriseva, Malin Akerfelt, et al.. Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields. PLoS ONE, Public Library of Science, 2015, 10 (12), ⟨10.1371/journal.pone.0143798⟩. ⟨cea-01820366⟩

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