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. 2022 Jun 28;9:370. doi: 10.1038/s41597-022-01450-y

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© The Author(s) 2022

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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Fig. 2 — The process of creating annotations on the WSI. First, the local, free-hand annotations are marked on WSI. Then, the annotations are exported as binary masks which get processed into categorized patches with the described filtering, see Algorithm 1. (a) Screenshot from QuPath v0.1.2 from the viewpoint of the annotator. The surrounding cyan-blue line indicated the area that was annotated. The various smaller colored regions represent different labeled areas. A tissue area without any annotation is considered normal. (b) The exported binary, black&white masks for the annotations. (c) Visualization of patches on a WSI. Patches that did not pass the quality filter are discarded and patches that had more than half of their pixels labeled with an annotation are assigned to that category. For the shown example 186 patches were kept. (d) A few examples of the resulting 512 × 512 pixel size patches. Each patch covers a 248 μm × 248 μm area.