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Cytomine_GetAnnotation

This repo shows how can we export annotations(mask) and corrosponding images(patches of whole slide images) from a Cytomine server.

Alt text

You should have a Cytomine server and install the Cytomine python client package first. I have modified the official version, and made it compatible for Python 3. You can find it HERE

Q&A:

  1. How can I get the enviroment variables, such as CYTOMINE_HOST and CYTOMINE_PUBLIC_KEY?

    Ask your Cytomine server manager.

  2. What's "url base address",and how can I know it?

    "Url base address" is associate with your Cytomine server. Our code will use this url address and some other information(image.fullPath) to piece together a full url to download an original image. You can refer to the last couple of lines in export_annotations.py. Login to your Cytomine server, open a project,and you will find a list of images. Find the download selection in the dropdown combbox, right click and save the link.Run conn.fetch_url("link you just copied") in your code,you will get the "Url base address" in the console. There might be more efficient ways to get it, tell me if you find it.

Contributors:

Jiang Jun and Hart Steven at Mayo Clinic