Here's another way round it.
Use the "File Name" variable in the Filter Rule "Aperture" to filter for text in your file name. Set these up as Smart Albums, and then use keywords to tag your images. (And you can nest your keywords, e.g.: "Stains" as a keyword group, and "HE" and others as children of this parent. You could even do "Magnifications" and "10x", "20x", "100x" etc. In general, keywords provide much greater administrative utility than custom fields.)
Are the images already in Aperture, or is this something you want to do on import?