I have many documents per day that are photographed and I need to organise by QR code. The problem is, zbarimg is struggling to pick up many of the QR codes in the photos, so I have been trialling processing them with imagemagick first, using morphology open, thesholding, etc, which has yielded much better results. The only issue with this is these apply to the whole image, which makes the rest of the file unusable for me, as I deal with the rest of the image based on colours and information which all gets destroyed in the processing. Could anybody give me an example on how I could apply my imagemagick filters to only a part of an image (coordinate based is fine) and leave the rest of the image untouched, so I can continue my process? I will be applying this to all images in a folder, so it's a batch file running this for me in most instances.
I have tried using crops, however this obviously leaves me with only the cropped portion of the image, which doesn't actually help when trying to process the rest of the file. I'm running my scripts on Windows 11, if that means anything in terms of the solution. Many thanks! Tom
EDIT:
Thank you all for the advice given! I solved my problem using the following:
convert a.jpg ( -clone 0 -fill white -colorize 100 -fill black -draw "polygon 500,300 500,1500 1300,1500 1300,300" -alpha off -write mpr:mask +delete ) -mask mpr:mask +repage -threshold 50% -morphology open square:4 +mask c.jpg
I did post this as an answer, but (and I have no idea why, I'm brand new to stack exchange) my answer was deleted. I used the clone to make the mask with the coordinates needed, then added the threshold and morphology that would make my QR codes more legible!
Thanks again everyone, really helped me out on my journey to figure it out :D

You can use
-regionto specify a region to process. So starting with this:You can then specify a region to colorise with blue and then change the region to blur part of the blue and part of the original: