GRAPHIE: graph based histology image explorer

BMC Bioinformatics
Hao DingRaghu Machiraju

Abstract

Histology images comprise one of the important sources of knowledge for phenotyping studies in systems biology. However, the annotation and analyses of histological data have remained a manual, subjective and relatively low-throughput process. We introduce Graph based Histology Image Explorer (GRAPHIE)-a visual analytics tool to explore, annotate and discover potential relationships in histology image collections within a biologically relevant context. The design of GRAPHIE is guided by domain experts' requirements and well-known InfoVis mantras. By representing each image with informative features and then subsequently visualizing the image collection with a graph, GRAPHIE allows users to effectively explore the image collection. The features were designed to capture localized morphological properties in the given tissue specimen. More importantly, users can perform feature selection in an interactive way to improve the visualization of the image collection and the overall annotation process. Finally, the annotation allows for a better prospective examination of datasets as demonstrated in the users study. Thus, our design of GRAPHIE allows for the users to navigate and explore large collections of histology image datasets. We...Continue Reading

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Citations

Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf
Aug 8, 2017·Nature Methods·Denis SchapiroBernd Bodenmiller

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Methods Mentioned

BETA
MDS
biopsies

Software Mentioned

GRAPHIE
h based H istology I mage E xplorer or
R script
Apache
js
GRAP
D3
R
SHIRAZ ( System of Histological Image Retrieval and Annotation...
InfoVis

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