Issue with extracting patches in magnificent level - x10

[YallapragadaG]

Describe the bug
When extracting the patches in magnificent level - 10x, I have got few images in black colour with stripes and few images are not clear. And when I tried extracting in x20 they were fine. I am just wondering why the difference ?

I have attached the patches with x10 for your reference.

[jgamper]

Hi @YallapragadaG - could you please follow the defined issue raising format.

It would be easier for me to diagnose if you could share the code snippet that you run to produce these results. The more information I have the better.

[YallapragadaG]

Hi @jgamper Thank you so much for the response.

I have tried simple pipeline with Otsu masking and tiling with magnificent level - 10 and patch size = 224.
please find the attached code snippet.

[jgamper]

Okay - I see you are running tcga! @YallapragadaG could you please tell me the slide name, and I will try reproducing your exact steps and see what I get 👍

[YallapragadaG]

Hi @jgamper

I have got slides from cbioportal(please find the link below) . But I donot remember which slide has given me the issue with 10x . I will try to recreate and let you know.

https://www.cbioportal.org/study/clinicalData?id=meso_tcga_pan_can_atlas_2018

Thank you so much.