Annotated necrosis and mitotic figures on 230 rat liver slides of the Open TG-GATEs dataset

<pre># Annotated necrosis and mitotic figures on 230 rat liver slides of the Open TG-GATEs dataset This dataset contains polygonal annotations of 230 whole slide images of the Open TG-GATEs dataset. The annotations were created by Bayer pathologists in a project collaboration between Bayer Pharmaceuticals and Aignostics GmbH. ## Dataset Files This dataset contains only text files which are referring to whole slide images of the Open TG-GATEs dataset. The images are not distributed with this dataset. Image URLs and their respective `md5` checksums are stored in `slides.json`. The annotations are available in the raw json format used in the collaboration as well as in converted [`geojson`](https://geojson.org/) format for easy import into other tools. | file | description | |:-----------------------------------|:-------------------------------------| | slides.json | URLs/md5-checksums of each slide | | annotations/raw/\*.svs.json | original format tissue annotations | | annotations/geojson/\*.svs.geojson | tissue annotations in geojson format | ## Annotated Lesions / Classes The dataset was annotated by 6 expert pathologists with the goal of labelling &quot;Necrosis&quot; and &quot;Mitotic Figures&quot; on rat liver whole slide images. Additional areas in the slides were labelled to improve model training. An overview of the annotated classes is given in the table below: | label | count | area (px^2) | |:---------------------------------------------------|------:|-------------:| | Necrosis (area) | 1576 | 386769004.0 | | Necrosis (single cell) | 1497 | 1624837.5 | | Mitosis | 5205 | 9322482.0 | | Single cell necrosis/apoptosis | 1531 | 1446001.0 | | Central vein | 1125 | 27947588.0 | | Connective tissue | 63 | 8478992.5 | | Dark hepatocytes | 763 | 2516812.5 | | Extramedullary hematopoiesis | 73 | 189508.0 | | Hemorrhage | 142 | 2231979.0 | | Inflammatory infiltrate | 1382 | 9859337.5 | | Large vessels | 224 | 597148962.0 | | Neoplasia | 176 | 478842.5 | | Oval cell/bile duct proliferation | 47 | 1621104.5 | | Parenchyma | 3249 | 673395978.0 | | Portal tract | 1067 | 40819943.0 | | Other lesions | 5 | 9251.0 | | Staining, contamination, and out-of-focus artifact | 46 | 4484697.0 | The pathologists labeled the following number of lesions: | pathologist | annotations | |:--------------|------------:| | pathologist-0 | 15660 | | pathologist-1 | 1749 | | pathologist-2 | 660 | | pathologist-3 | 79 | | pathologist-4 | 22 | | pathologist-5 | 1 | ## Reference The 230 slides of the Open TG-GATEs Pathological Image Database which the annotations refer to are part of the `Toxicogenomics Project and Toxicogenomics Informatics Project under CC Attribution-Share Alike 2.1 Japan` (`CC-BY-SA-2.1-JP`) and are available for download via [10.18908/lsdba.nbdc00954-02-000](http://doi.org/10.18908/lsdba.nbdc00954-02-000). ## License All `*.json` and `*.geojson` files in this distribution are licensed under the same `CC Attribution-Share Alike 2.1 Japan` (`CC-BY-SA-2.1-JP`) license as the Open TG-GATEs Pathological Image Database. The license text is included in the file `LICENSE` in the distribution archive. ## Acknowledgements We thank Dr. Maximilian Alber[^5], Oliv&eacute;r Atanaszov[^5] and Dr. Sharon Ruane[^5] for providing support, the annotation platform, the model training infrastructure and for the great collaboration. We also thank Dr. Yoshinobu Igarashi[^6] for providing insight and advice regarding the dataset and its licensing. [^5]: Aignostics GmbH [^6]: National Institutes of Biomedical Innovation, Health and Nutrition - Toxicogenomics Informatics Project </pre>