Question: Quantification of epidermal thickness in H&E stained sections

Hi All,

I have been trying to work out how to quantify the average thickness of epidermis in my H&E stained sections. The background is that I have grown skin a skin equivalent, and performed different treatments whilst the skin equivalent was growing. The skin was then fixed, sectioned and H&E stained and imaged and I am now trying to quantify if growth has been impaired. However, I am very new to this (molecular biologist out of their depth!), so any pointers as to how to do this would be gratefully accepted!

Images are currently in .czi format, and I have been looking for a way to quantify the average thickness in either qupath or image J. I have copied in an example image below.

So far on qupath I have tried Analyse --> Preprocessing --> Simple tissue detection. Whilst this has allowed me to annotate my area of interest (see below), I haven’t managed more than this.



The last time I had to do something similar, I used the line tool a lot, and then averaged the line lengths…

To do anything more automated, you would probably need to code some way to know the orientation of the annotations, and then draw a line perpendicular to that at intervals. If I think of anything better I’ll post, but depending on how many samples you have, you might want to dive in with the line tool.