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A Containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

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posted on 2023-03-31, 01:46 authored by Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurc
<p>Video describing the containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images</p>

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ARTICLE ABSTRACT

Well-curated sets of pathology image features will be critical to clinical studies that aim to evaluate and predict treatment responses. Researchers require information synthesized across multiple biological scales, from the patient to the molecular scale, to more effectively study cancer. This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features. All the services are deployed as containers and the user-facing interfaces as web-based applications. The set of containers and web applications presented in this article is used in cancer research studies of morphologic characteristics of tumor tissues. The software is free and open source. Cancer Res; 77(21); e79–82. ©2017 AACR.

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    Computational MethodsAlgorithmsDatabase resourcesSoftware

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