YES, using DAPI in your fluorescence staining is strongly prefered (or another nuclear staing, please reach out to us to discuss other options if DAPI is not compatible wtih your experiment)- DAPI works fabulously with the autofocus of the slide scanning system and can significantly improve the quality of the focus across your samples. However, DO NOT use it in your mounting medium. It is much better to use DAPI as part of your staining protocol and to do some washes afterwards. DAPI in the mounting medium will cause a haze across the background - minimizing your signal to noise and making it more difficult to identify cells using analysis software and also negatively impacting your image quality.