After command "clear outside" the outselected area has non-zero value

Hello! I am trying to quantify the fluorescence intensity around the cell cortex using Asimuthal plugin. For this I need to select an object using the polygon tool and then use the command “clear outside” to remove all the rest and to bring the surrounding area background to 0 value. However after implementing the command I get a green background with the Value 255 as can be seen on FIJI menu. The program is recently downloaded and updated, and I have the same issue with Imagej. Does anyone know how to remove this bug? Thank you a lot in advance!

Hi Ilya,
Looks like your image has two channels based on your screenshoot. I suspect that your selection is associated with one of the two channels and when you run the ‘clear outside’ command, only that channel is being cleared. Try switching between the channels (use slider at bottom of image) and see what the background values are on the other channel. They are probably 0.
In order to resolve the issue, it would be useful if you could provide a sample image and enough information to reproduce the problem (e.g. a starting sample image and all the steps that lead to the problem).
Hope this gets you on the right track.


Hi Volko, I am working with z-stack obtained at Zeiss axioscope, zvi format. My goal is to find mosaic cells in max intensity projection of z stack, isolate them using selection tool and analyze the intensity along the radius using azimuthal average plugin. It turned out however that it was not a background from the second channel, but what the exact reason of the background was I am still not sure. Anyway, it looks like I was able to solve the issue for now, by converting the image into 8 bit type, then after command “clear outside” background becomes 0. Anyway, it seems to to work now and thank you for replying!