Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Usage readme #11

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Usage readme #11

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c4ba72a
add instructions for wsi label upload
sinberlin2 Jan 17, 2022
a05c152
made json dumps a bit clearer
sinberlin2 Jan 18, 2022
df1b281
added level 0
sinberlin2 Jan 19, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 28 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 ([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.
- 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