add slide / wsi folder - Githubissues

delta2golf commented 2 years ago

WSI should be placed in which folders? I have tried different folders. In the frontend, in the add slides form I am getting "Path does not point to a file". Input example /slide/80b306aa-cd5e-7579-f77b-215a80eff300_154138.svs

smistad commented 2 years ago

Hi @delta2golf, the path should be an absolute / full path to your wsi file

delta2golf commented 2 years ago

Thank you. The full path does not work. The computer is a mac. Request Method:	POST

http://127.0.0.1:8000/slide/add/ 3.2.10 RuntimeError Failed to load slide image pyramid from /Users/delta2golf/Downloads/2021-30/15ba3af0-b2f5-8704-6559-bd24cf373fc6_154006.svs

smistad commented 2 years ago

We have not tested the system on Mac yet, we mainly use ubuntu linux. It is failing here: https://github.com/AICAN-Research/learn-pathology/blob/master/slide/models.py#L41

Perhaps FAST/dependencies is not installed correctly? To install FAST on macOS, make sure you have all the necessary requirements:

macOS 10.13 or newer. Only intel (x86_64) architecture is supported atm.
Install homebrew if you don't already have it. Install the following packages using homebrew: brew install openslide libomp

AICAN-Research / learn-pathology

add slide / wsi folder #9