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Added a file with all download links
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ChristianMarzahl committed Nov 26, 2021
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Expand Up @@ -109,3 +109,4 @@ SDATA/Inference/test_TrainSREP-V2-Ablation.py
SDATA/Inference/test_TrainSREP-V2.py
SDATA/Statistics/EIPH_Annotations.pkl
MIDL2021/Slides/*/*
/SDATA/EIPH WSI screening.xlsx
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12 changes: 11 additions & 1 deletion SDATA/README.md
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Expand Up @@ -46,7 +46,7 @@ The dataset can be examined at [EXACT](https://exact.cs.fau.de/) with the userna
## Start and Structure

- Please install the [requirements.txt](requirements.txt) ```pip install -r requirements.txt```
- Download the slides [Download.ipynb](Download.ipynb)
- Download the slides [Download.ipynb](Download.ipynb) or download individual files with the EXCEL [file](Paper/FilesAndLinks.xlsx)
- Install Openslide for Linux ```!apt-get install python3-openslide``` or Windows https://openslide.org/download/
- The folder [Statistics](Statistics) contains notebooks which analyse the dataset annotations
and general information about the slides
Expand All @@ -57,6 +57,16 @@ maps
- [Cluster](Cluster) contains code to create custom annotation maps and synchronise the generated images and annotations with
EXACT.

## Annotation formats

The annotations for the cells are available in different formats.

- [SQLite](Statistics/SDATA_Final_Annotations.sqlite) for [SlideRunner](https://github.com/DeepPathology/SlideRunner)
- [Pickle](Statistics/SDATA_Final_Annotations.pkl)
- [CSV](Statistics/SDATA_Final_Annotations.csv)

The following EXEL [file](Paper/FilesAndLinks.xlsx) contains the links to download the individual files. For an automated download, please follow the instructions at the ***Start and Structure*** section.

### Notebooks

| Section | Species | Name | Describtion |
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