Appion

tested and found several issues:

testing the parameters does not work
it runs but there is no way to evaluate whether it is doing a good job or not as one can not see the actual masks
I tried to circumvent this by creating a stack that was masked and then convert the stack into picks which could be displayed in the image viewer but the mask run does not show up as an option during stack creation

I think this is an extremely valuable tool if it would work - especially as we always clip some carbon in the image - for now its probably the best to remove it from the webpage