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Robust 3D cell segmentation by local region growing in convex volumes


Pfister, Sabina Sara; Betizeau, Marion; Dehay, Colette; Douglas, Rodney (2013). Robust 3D cell segmentation by local region growing in convex volumes. Proceedings of the International Symposium on Biomedical Imaging:426-431.

Abstract

Clustering of cells is based on their expression profiles (either volume, average expression, standard deviation, sum, median or Pearson correlation coefficient). As an example, the hierarchical clustergram of median expression values was computed on 8343 cells in the germinal layers of monkey developing cerebral cortex stained for Pax6 (red), Tbr2 (blue), Ki67 (green), and nuclear staining DAPI. Cells where clustered with the standard k-means algorithm, whereby the number of clusters k=6 was determined empirically.

Abstract

Clustering of cells is based on their expression profiles (either volume, average expression, standard deviation, sum, median or Pearson correlation coefficient). As an example, the hierarchical clustergram of median expression values was computed on 8343 cells in the germinal layers of monkey developing cerebral cortex stained for Pax6 (red), Tbr2 (blue), Ki67 (green), and nuclear staining DAPI. Cells where clustered with the standard k-means algorithm, whereby the number of clusters k=6 was determined empirically.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Neuroinformatics
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2013
Deposited On:13 Feb 2014 14:08
Last Modified:08 Dec 2017 08:07
Publisher:Institute of Electrical and Electronics Engineers
ISSN:1945-7928
Additional Information:ISBN: 978-1-4673-6456-0
Publisher DOI:https://doi.org/10.1109/ISBI.2013.6556503

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