These are chat archives for fiji/fiji

Feb 2018
Feb 02 2018 03:52 UTC
Hello all. I'm an absolute beginner with ImageJ/Fiji. I've been able to apply a few useful built-in tools to my CT scans, but many of the filters fail because my images have a background. The kind of images I look at can be found here: As you can see, anything outside the inscribed circle is useless background. My question to the community is: How do you suggest I get rid of this background? Can I do this using the existing functions, or do I have to write my own script or plug-in? (additional detail that may be of help: for my purposes, it would be OK to merge the background with the dark, textured parts at the top and bottom of the disk.) Thanks in advance!!
Ellen TA Dobson
Feb 02 2018 14:32 UTC
Hey @jfcollard - this is a great question for the ImageJ Forum - would you mind posting it there??
Curtis Rueden
Feb 02 2018 16:03 UTC
@jfcollard The basic idea would be to generate a circular ROI covering the area of interest, and nothing else, and then do your filtering on that. If you can avoid drawing the circle by hand, it is much better/faster/reproducible. But for detailed discussion of how to proceed I agree with @etarena that the forum is the best place.