Bulk annotations viewer ¶
By: aalva3 on April 19, 2022, 2:26 p.m.
How can we view annotations for bulk images (specifically the data present in data/WSIBULK/annotations/masks)?
Bulk annotations viewer
Re: Bulk annotations viewer ¶
By: mart.vanrijthoven on April 19, 2022, 2:33 p.m.
Dear Ashley Lenilla Alva,
You can view the tumor bulks over the images with the ASAP software: https://computationalpathologygroup.github.io/ASAP/ . You can download the latest version here: https://github.com/computationalpathologygroup/ASAP/releases/tag/ASAP-2.0-(Nightly). You can open the image and the mask as an overlay.
Alternatively, you can also open the mask with python libraries. Please see the code section for more info: https://tiger.grand-challenge.org/Code/ Please note that openslide-python will not be able to open these masks. Thus for the wholeslidedata package, you will have to use ASAP or Pyvips backend.
Best wishes, Mart
