This post is mainly motivated by laziness, and my current inability to write scripts in groovy…: I am looking for a way of easily export snapshots from multiplexed IF images within QuPath, including the overlay image and each single colors (without including any annotation or analysis features… simply the image). It is pretty long to do manually when taking many snapshots (especially ticking off each channel to have single colors and overlay etc.), and I feel I (and certainly others) would greatly benefit from such feature.
Here is a bit more details of what I would like to do: say I navigate through a slide/tissue, and find a region of interest. I go to the preferred magnification and ideally I would like to be able to run a script that would automatically export what is seen in the middle of the viewer:
- for example at a defined size (e.g. a square of 1024*1024px)
- of the overlay+single colors
- in a directory with a structure like “filename_snap1_overlay.png” “filename_snap1_channel1.png” “filename_snap1_channel2.png” etc… (I assume exporting .tiffs would be irrealistic?)
- ideally with the option of including the size bar information…
I know it sounds like I am looking for a sort of graal… does this sound feasible? or has anyone already written/used similar script?
Many thanks in advance for your help