2D class with reference input

Gray area here,

but is there a way in any program to include 2D templates as reference for 2D classification? I have particles which are very often not found as a class, which I have been lucky enough to see as an obviously correct 2D class with optimized parameters (16Å max res align namely). Since the class exists I know the view is in the data but missed in all other classification attempts. Would be great to give a starting template to improve the alignment. Fish for 2D classes from crazy heterogeneous data.