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@@ -10,3 +10,31 @@ 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 (j.hudecek@nki.nl) 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 "user_name@nki.nl" --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.
+  - Using json.dumps(), you can transform your list of annotation dictionaries into a sting in the format above. 
+  - 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). The coordinates need to be given at level 0 which corresponds to the entire view of the whole-slide image.
+  - The
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