These are chat archives for fiji/fiji

Feb 2018
Feb 02 2018 03:52
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 T Arena
Feb 02 2018 14:32
Hey @jfcollard - this is a great question for the ImageJ Forum - would you mind posting it there??
Curtis Rueden
Feb 02 2018 16:03
@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.