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. 2019 May 15;9:7449. doi: 10.1038/s41598-019-43525-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Application of trained CNN to whole-slide images in an optimized patch-based approach. (A) Raw image including CD3+ cells and non-specific stain, (B) overlay of the cell segmentation with potential CD3+ cells in green and 80 × 80 pixel grid, (C) relevant patches (red) identified based on positive cells in (B,D) prediction result of the CNN (violet: CD3+, red: non-specific stain).