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J Comput Biol. 2013 Aug;20(8):583-92. doi: 10.1089/cmb.2013.0025. Epub 2013 Jul 3.

ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.

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1
Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, Utah 84112-5330, USA.

Abstract

ImagePlane is a modular pipeline for automated, high-throughput image analysis and information extraction. Designed to support planarian research, ImagePlane offers a self-parameterizing adaptive thresholding algorithm; an algorithm that can automatically segment animals into anterior-posterior/left-right quadrants for automated identification of region-specific differences in gene and protein expression; and a novel algorithm for quantification of morphology of animals, independent of their orientations and sizes. ImagePlane also provides methods for automatic report generation, and its outputs can be easily imported into third-party tools such as R and Excel. Here we demonstrate the pipeline's utility for identification of genes involved in stem cell proliferation in the planarian Schmidtea mediterranea. Although designed to support planarian studies, ImagePlane will prove useful for cell-based studies as well.

PMID:
23822514
PMCID:
PMC3728726
DOI:
10.1089/cmb.2013.0025
[Indexed for MEDLINE]
Free PMC Article
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