Netcdf isn't an image format, it's a gridded data storage format. So you'll have to give us more information about the data in those files (dimensions?) for us to help. I suggest looking at the documentation fornetcdf,ncread, etc. as well asgeotiffwrite.
Kind of hard to guess since you didn't attach any of the images. But I'd try to add them all up and then use rgb2ind(). If they are uint8 you'll have to cast to uint16 first. Or you mgiht try binarizing them first. Or cast them to double and add them up and divide by the number of images and then cast back to uint8, and then use rgb2ind. Like I said, hard to say until I see your images and you/I try some things.
Best Answer