It seems to me that [A] isn't actually the matrix itself, but rather the name it is given in the software program. Because they are embedded within a paragraph, I suggest that you use the usual square brackets. By the way, since this is dealing with a software program, is any of the material transcribed using Computer Braille? Generally anything that has to be entered into a field in the software program (i.e., keyed by the reader), should be transcribed in Computer Braille. You would probably have a better understanding of whether or not this is the case, based on the figure numbers that are referenced in the text.