This is something which had worried me from the start.  We had three different images(freqs), but used the same depth lines for them.  If they have different sizes then what is the size of the depth line?  The original line model only had a freq dictionary for the intensities but everything else was just in a list.  One option is to just clip all arrays to the size of the smallest intensity image (where there is a difference).  Missing one column on the edge of an image here and there shouldn't matter and would make everything else easier.