Long time user, new poster!
I’m looking into how different tissue processing techniques affect the final outcomes of immunohistochemistry. One of the parameters I’m looking at will be DAB staining intensity. I thought QuPath could help solve this quickly with a batch process.
My idea is to create a script that performs automated tissue detection, cell detection, then exports the detection measurements. I’ll then look at the range (Max and Min) of all measurements on each slide. I’ll have a range and a mean DAB Max to use per technique.
I have hundreds of slides to analyse, so I’m hopeful that even though I’m not analysing serial sections, I can get an idea of if the DAB staining is in any way impacted by these different techniques. I also have multiple antibodies to test and on several different tissue types.
I have a few questions:
Should I set the stain vectors automatically per slide, set the stain vectors to a specific slide, or not assign them at all? I’m wondering if not assigning the stain vectors would give an arbitrary baseline, as all I’m looking at is DAB intensity.
Is cell detection the best way to define the detection area? Could a pixel or SLIC based ‘tiling’ give me better workflows or more streamlined data?
I’m currently working on the old version of QuPath as I’m on a University computer and can’t update with without IT Permissions, so I’m appreciate legacy type instructions. Suggestions for the new milestone QuPath version obviously welcome for when I get it updated but just a note to say I can’t test these methods at this point…