Set brightness and contrast

[Al]

Hi Qupathers,

Great work on this software and really appreciate the recent video tutorials uploaded.

I have multichannel fluorescent tifs which I adjust the min/max setting in brightness and contrast in order to remove background staining. However the the issue I'm having is that the analysis (e.g. cell detection) seems to analyse the original image and not the altered one. In imageJ there is a "set" button which locks the changes made in brightness and contrast for analysis, is there a way to do similar in qupath? 

Thanks,

Alan 

[micros...@gmail.com]

QuPath does not adjust the images, though by using the ImageJ macro runner, you could repeat any ImageJ code over a large area.

https://github.com/qupath/qupath/wiki/Working-with-ImageJ

If all you are doing is changing the brightness and contrast, you should be able to raise your thresholds instead to get the same result. I don't think there is a difference between a background of 100 and a threshold of 150, or locking an image to -100 and having a threshold of 50. Unless you are interested in variations in the background, or the background varies... in which case adjusting the brightness and contrast would also not work.

[Al]

THanks micros