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Usage readme #11

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add instructions for wsi label upload
sinberlin2 Jan 17, 2022
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made json dumps a bit clearer
sinberlin2 Jan 18, 2022
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add instructions for wsi label upload
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sinberlin2 committed Jan 17, 2022
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Expand Up @@ -10,3 +10,30 @@ Utilities and command-line interface to interact with the [SlideScore](https://s
- Python SlideScore API client
- command-line utilities
* For downloading from and uploading to SlideScore.


## Guide to using the slidescore API
For uploading or downloading labels or whole-slide images, the following steps need to be undertaken:
- Contact Jan ([email protected]) to obtain an API token which allows you to access the slidescore or rhpc server. You need to give the following information: study_id(s), upload download or both, server: slidescore or rhpc server on which the study is located
- Export the token to as an environment variable (every time you access our server) and also when you switch between accessing the slidescore or the rhpc-slidescore server : <pre><code> export SLIDESCORE_API_KEY=”your_token”</code></pre>
- use slidescore-api command

### Example command for uploading labels:
<pre><code> slidescore --slidescore-url "https://slidescore.nki.nl" --study "818" --disable-certificate-check upload-labels --user "[email protected]" --results-file "path_to_file/file.csv" --csv-delimiter "," </code></pre>
- short flags do not work properly at the moment)
##### Requirements for the labels file:
- format: csv
- separator: default is tab “/t”.
- Every whole-slide image is one line.
- Csv columns are: "imageID", "imageName", "user", "question", "answer", however no header should be present in the annotation file.
- If you do not have the imageID or imageName the mapping for this can be copied on slidescore under: → study → export cases.
- imageID: type string
- imageName: type string
- question: type string
- Refers to the type of label, e.g. ducts or lymphocytes.
- This question needs to be added to the study on slidescore: go to → study → edit study → questions → select question type e.g. annotate shapes for bounding box → name the question by clicking on it after it appears under "scoring sheet". The colour of the annotation can be also changed here.
- answer: type string
- Needs to be in a very specific format: “[{annotation 1}, {annotation 2}, {annotation n}]”. This list is inside the string.
- It can be achieved with using json.dumps(wsi_results)
- Every annotation is also in a specific format.
- For rectangle annotations: {"type": "rect", "corner": {"x": 123, "y": 456}, "size": {"x": 12, "y": 34}}. The corner coordinates refer to the top left corner of the rect. The size coordinates refer to the width (x) and the height (y).