I’m trying to (batch-) export tiles from multichannel fluorescence images (different proximity ligation assay dots, DAPI) in order to use these tiles to train a neural net to recognize the dots. The tiles should be rendered Images, as I intend to train the network on false colours (e. g. red dots vs. green dots).
I am not familiar with groovy. Fortunately until now I could always find a right script on the excellent Pete’s QuPath-webpage or here in forum for which I am very thankful to the authors of the scripts.
This time I also found a Pete’s script which generates whole size rendered images (Script to export a rendered (RGB) image in QuPath v0.2.0 · GitHub). This script which works fine with QuPath 0.2.3. However, I could not figure out, how to change the script to get small tiles (e.g. 256x256) of the manually defined larger regions (e.g. rectangle annotations or tissue outlines).
Could anyone be so kind to advise me on how to change the above mentioned script? Or should I better take the whole size images and tile them with another software?