I want to scan for HPV and use a cotton sample with vaginal liquid and this is going to be relatively dry. Do I wash the cotton with water or spirit and use this in the digitizer?

You may be able to spread the cotton so it is thin and covers the slide, but cotton would introduce a thickness which would increase errors. So for your case it may be better to use distilled water to dissolve any matter on the cotton, and swab the water between the slides. 

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