Metrics definitions

[suminwei]

Hi,

I was wondering if there is document that explains what each metric being quantified by HistoQC means (for instance - grayscale brightness. chan1_brightness, chan2_brightness, rms_contrast, final_energy)?
I'm currently trying to understand what variables are different between the samples I'm looking at.

Thank you!
Lisa

[choosehappy]

unfortunately, no official document, but i'm hoping that almost of them are self-explainatory e.g. , grayscale brightness is exactly that, the grayscale brightness of the tissue region if you're familiar with python code, you can search the github repo for any of the variable names, and it'll point you at the 2 or 3 lines of code used to generate that particular feature - histoqc was developed in this modular way to enable facile understanding of the "stuff under the hood Message ID: ***@***.***>