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

# 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
"Necrosis" and "Mitotic Figures" 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], Olivér 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