jnkather / deep-stroma-histology Goto Github PK
View Code? Open in Web Editor NEWConvolutional neural networks for extracting a "deep stroma score" from histological images of human cancer
License: MIT License
Convolutional neural networks for extracting a "deep stroma score" from histological images of human cancer
License: MIT License
Thank you for your hard work and code sharing. But I found that I cannot reproduce your result in Fig 5. After running your SCORE_APPLY_v1.R script, I got CAF score, Stage I-IV equal 0.772, which is not equal to your result in Fig 5. please help!
The link to the "color normalization toolbox" (https://warwick.ac.uk/fac/sci/dcs/research/tia/software/sntoolbox/) is currently redirecting to the login page, making it inaccessible. I was able to find following alternative link (https://warwick.ac.uk/fac/cross_fac/tia/software/sntoolbox/), but I am not sure if this is the used implementation.
Could you kindly share the original toolbox used within the repository to facilitate proper utilization and reproducibility? Thank you.
for example, TCGA-CM-6675-01A-01-TS1.2bea1d2f-2ed2-4179-a3e3-2ea1c135d638.svs, the percent_stromal_cells in your paper is 12%, but in TCGA GDC I found the value 10%. I wonder if it's because the update of TCGA website? looking forward to your reply.
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