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The use of methylene blue, although popular in breweries, has been shown to be inaccurate when counting cells of ''Brettanomyces''. Trypan blue staining has been shown to give more accurate cell counting results <ref name="Hubbe" /><ref>[https://www.facebook.com/groups/MilkTheFunk/1407620505932826/?comment_id=1407723619255848&comment_tracking=%7B%22tn%22%3A%22R8%22%7D Discussion with Richard Preiss regarding counting Brettanomyces with methylene blue versus trypan blue staining. 09/15/2016.]</ref>.
One of the problems with cell counting for ''Brettanomyces'' is that they tend to form pseudohyphae (elongated cells that are attached to one another) during growth. This makes counting the cells difficult. Martyniak et al. (2017) has proposed a new way of counting cells for ''Brettanomyces'' by using the fluorescence capability of a Nexcelom Cellometer where the AO/PI stains only the nuclei of the individual cells <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/1362220137139530/ Brian Martyniak. Milk The Funk thread on counting ''Brettanomyces'' cells. 06/29/2016.]</ref><ref>[https://link.springer.com/article/10.1007/s10295-016-1861-4 A novel concentration and viability detection method for Brettanomyces using the Cellometer image cytometry. Brian MartyniakJason BoltonDmitry KuksinSuzanne Martyniak, Jason Bolton, Dmitry Kuksin, Suzanne M. ShahinLeo Shahin, Leo Li-Ying Chan. 2017.]</ref>. It has been observed that pseudohyphae might be less common in ''Brettanomyces'' cultures that have been grown in wort versus lab media, making them easier to count <ref>https://www.facebook.com/groups/MilkTheFunk/permalink/1362220137139530/?comment_id=1932020246826180&comment_tracking=%7B%22tn%22%3A%22R%22%7D Caroline Whalen Taggart. Milk The Funk thrad on Brettanomyces cell counting. 12/26/2017.]</ref>.
====Example of a Home Lab Orbital Shaker====