Detection of stained area without counting cells

Hi all,

Does anyone know if there is a way in QuPath to quantify the detection of DAB relative to the total area?

I would like to analyze this kind of IHC-stainings (specially in brain but also in other type of organs) but it is very hard to count these cells because of the specific (and different) shapes. Previously we analyze this kind of IHC-stainings with QWin to detect the stained area.

Does anyone have experience with this, or perhaps another way to quantify this?

Thank you!




This can be done with Positive pixel count, which has been available since earlier versions of Qupath. I have used it a lot to quantify % DAB area and it works, but it can be slow and have issues when trying to analyze very large areas. More recently “Create simple thresholder” was added and I think the plan is for it to replace Positive pixel count as it works better, but at this time in brightfield images the channels available do not include hematoxylin and eosin, or DAB and hematoxylin. I’m impatiently waiting for this! :slightly_smiling_face:


This is indeed an option to measure and it seems that QuPath take it precisely so thank you!! :grin: :grin: