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choosehappy / HistoQC

HistoQC is an open-source quality control tool for digital pathology slides
BSD 3-Clause Clear License
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Metrics definitions #314

Open suminwei opened 1 month ago

suminwei commented 1 month ago

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 commented 1 month ago

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

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