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Backend set to tiffslide, but openslide is used #225
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hi @vthorsson - thanks for reporting this issue. i'm able to reproduce it. i have opened #226 as an attempted fix. i will wait for the continuous integration to run if you want to try before i merge, please feel free to install from that branch:
i wanted to also tell you i greatly enjoyed your 2018 immunity paper on the immune landscape of cancer. could you please tell me, is it possible to calculate tumor mutational burden from supplementary table 1? |
Thanks for addressing this so quickly @kaczmarj - look forward to trying out the fix! Thanks for the good words on the Immune Landscape manuscript. You can find the TMB on the associated publication page |
@kaczmarj from my tests using the install from the branch provided above I get the sense that
|
thanks. i am fixing this in another branch now. use this to try it out:
when i originally wrote |
Thanks @kaczmarj , things are looking good now!
BTW, this particular ome.tiff was exported from QuPath, from an imported .svs ! (I may check if the wsinfer results are similar ). Related: Do you have any material posted on requirements/desired characteristics for WSI image files as input for wsinfer? |
fantastic! and to answer your last question, we don't have any material posted about requirements/desired characteristics for WSI images. a few things come to mind however:
if you have anything else in mind, please do let me know. thanks again for finding this bug and reporting it! |
@kaczmarj thanks for the helpful pointers above. I am seeing some signs* of my tissue segmentation step failing possibly due to do high background, so I am working on pre-processing to remove background ( A future feature request: to be able to run only the tissue segmentation and ensure that the thumbnail looks OK) I apologize in advance as my questions largely seem a consequence of a not-ideal input file, but that led to a few things. In terms of specific file format questions/comments
Thanks again *the thumbnail looks off - it might be the detected 'boundary' is the entire slide |
Thanks for providing a really useful tool.
I have a wsinfer installation with both
openslide
andtiffslide
. When I select tiffslide on the command line, it looks like my input file is still opened withopenslide
.I can reproduce the error message if I manually open the file using openslide (
openslide.OpenSlide
), whereas as tiffslide opens it just fine (tiffslide.TiffSlide
).I'm wondering if I am misunderstanding the impact of
--backend tiffslide
or if this is expected or unexpected behavior.(The input file is an ome tiff, and I have been able to run wsinfer successfully on svs files with this same install. Installed using conda as per instructions)
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