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acsbal / Automated-TIL-scoring-QuPath-Classifier-for-Melanoma

QuPath TIL classifier for Melanoma on HE slides
GNU General Public License v3.0
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Classifier is predicting every detected cell as a lymphocyte #1

Open SWFarag opened 4 years ago

SWFarag commented 4 years ago

Hi there, I downloaded your classifier and applied it on an annotated melanoma whole slide image. The classifier predicted all detected cells as "lymphocytes". Could you please upload a detailed documentation how to use the algorithm just to make sure I am not skipping any important pre-processing step.

Thanks a lot in advance!

AshleyW22-lab commented 3 years ago

Hello, I am having a similar issue to the one noted above. Do you have any guidance on the workflow used along with the algorithm? I have tried following along with the methods outlined in the publication, but the classfier predicts all cells in my sample as "Immune cells".

Thanks for your help.

SWFarag commented 3 years ago

Hi Ashley,

Sorry for the late reply, the authors never really replied to my issue. But I believe the main issue has to do with columns (features) names. Meaning, you need to make sure that both the columns used in the paper's model and the columns used in your cell measurements are exactly the same.

Best, Sherif

AshleyW22-lab commented 3 years ago

Hi Sherif,

Thank you so much for the advice. I thought I had tried matching all of the features in the paper's model, but apparently I had not. Your suggestion worked!

Best, Ashley

SWFarag commented 3 years ago

I am glad, it worked!

Best,

Sherif

drmayoliu commented 3 years ago

Hi Sherif and Ashley,

Could you describe how to load and run the trained classifier "TIL_Melanoma_NN192.qpclassifier" in the QuPath? I tried to run it through the script editor with the following scripts but failed.

runClassifier("D:/Graduation/Automated-TIL-scoring-QuPath-Classifier-for-Melanoma-master/TIL_Melanoma_NN192.qpclassifier")

[ERROR] qupath.lib.scripting.QP - Could not load classifier from D:/Graduation/Automated-TIL-scoring-QuPath-Classifier-for-Melanoma-master/TIL_Melanoma_NN192.qpclassifier

Thanks a lot in advance! Best, Kyrie