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jonasteuwen authored Oct 21, 2023
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Dlup offers a set of utilities to ease the process of running Deep Learning algorithms on
Whole Slide Images.

Check the [full documentation](https://docs.aiforoncology.nl/dlup) for more details on how to use dlup.

## Features
- Dataset classes to handle whole-slide images in a tile-by-tile manner
- Annotation classes which can load GeoJSON, [V7 Darwin](https://www.v7labs.com/), [HALO](https://indicalab.com/halo/) and [ASAP](https://computationalpathologygroup.github.io/ASAP/) formats and convert these to masks.
- Command-line utilities to report on the metadata of WSIs, tile WSIs, and convert masks to polygons.
- Read whole-slide images at any arbitrary resolution by seamlessly interpolating between the pyramidal levels
- Dataset classes to handle whole-slide images in a tile-by-tile manner compatible with pytorch
- Annotation classes which can load GeoJSON, [V7 Darwin](https://www.v7labs.com/), [HALO](https://indicalab.com/halo/) and [ASAP](https://computationalpathologygroup.github.io/ASAP/) formats and read parts of it (e.g. a tile)
- Transforms to handle annotations per tile, resulting, together with the dataset classes a dataset consisting of tiles of whole-slide images with corresponding masks as targets, readily useable with a pytorch dataloader
- Command-line utilities to report on the metadata of WSIs, tile WSIs, and convert masks to polygons

Check the [full documentation](https://docs.aiforoncology.nl/dlup) for more details on how to use dlup.

## Quickstart
The package can be installed using `python -m pip install dlup`.
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- [ahcore](https://github.com/NKI-AI/ahcore.git): a pytorch lightning based-library for computational pathology

## Citing DLUP
If you use DLUP in your own research, please use the following BiBTeX entry:
If you use DLUP in your research, please use the following BiBTeX entry:

```
@software{dlup,
author = {Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus, E.},
month = {10},
title = {{DLUP: Deep Learning Utilities for Pathology}},
url = {https://github.com/nki-ai/dlup},
url = {https://github.com/NKI-AI/dlup},
version = {0.3.31},
year = {2023}
}
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or the following plain bibliography:

```
Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus E. (2023). DLUP: Deep Learning Utilities for Pathology (Version 0.3.31) [Computer software]. https://github.com/nki-ai/dlup
Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus E. (2023). DLUP: Deep Learning Utilities for Pathology (Version 0.3.31) [Computer software]. https://github.com/NKI-AI/dlup
```

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