I,ve tried to prepare a solution of 0.4% trypan blue in PBS filtered at 0.44 um but I still see precipitates. This does not let me see the cells correctly under a microscope.
I don't make my own trypan blue but I have a similar problem using an old stock purchased from invitrogen which is now close to finished and at the very bottom of the bottle there are a lot of precipitates/debris/clumps that make it difficult to count cells. Under the scope it doesn't look like salt crystals but rather stringy clumps. I have tried to get around the issue quickly just by pipetting some of the TB into eppendorfs or falcon tubes and allowing it to sit upright until ready for use so that the debris falls to the bottom, and when I need to use it I slowly take from the top of the solution to try and avoid pipetting up precipitates at the bottom. I have also thought maybe a quick centrifugation would work even better but I never bothered to take the extra time since just waiting for precipitates to settle to the bottom works fine for me most of the time. I have also thought of maybe heating but I wouldn't try this since pH and osmolarity will change with temperature and likely end up killing all cells...
I also bought a new stock so I don't have to deal with this again for a long time but I would still like to know if anyone else has experienced this, what is the cause and identity of the clumps, and if it does happen again how I could better eradicate the annoyance.