self.wsi out of scope from patchgen?

[mahmoodlab]

self.wsi out of scope from patchgen?

[nazim1021]

Hi tried, with presets False option and using bwh_biosy.csv, seems to be working now

[fedshyvana]

Hi, I have not actually encountered this problem before or seen it being reported so far. However, I have also not worked with a lot of .mrxs files.
Off the top of my head, it could be because of the "padding" option used (basically if the size of the patches does not divide into the dimensions of the WSI perfectly, the edges are padded). For now I would suggest editing one of the preset csv files (under presets/) you hope to use by setting the "use_padding" value from True to False, and then try to run the command with --preset flag, specifying the edited preset_file? If that does not solve the problem, I am happy to look into the issue if you share with me the slide that produces the error (although it might take me a couple of days to get to it).

[nazim1021]

ah i see. Thanks for prompt response. I ll try out the presets option, otherwise i can share the mrxs slide later