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The ANUEMU is a centrally funded campus wide facility, administered and supported by the Research School of Biological Sciences.

The John Curtin School of Medical Research and the Research School of Earth Sciences also maintain electron microscope facilities with varying access arrangements and links to the central Unit. An advisory group (MSTAG) monitors microscopy and microanalysis resources and requirements across campus.

Small to medium equipment is bought from operating funds and user contributions,  with any additional funds that can be gleaned from internal or external agencies.  Large equipment purchases are underpinned by the ANU EM Reserve (an accumulating fund) and more recently by external grant schemes such as ARC Linkage Equipment and Infrastructure, and NH&MRC.