Clean coverslips are important in Single Molecule Localization Microscopy because any background noise present on the glass can be detected and localized. While those spots can usually be removed with analysis filters, it is always better to start with the best sample.
From our experience, Ibidi chamber and properly maintained coverslips are clean enough for experiment.
But if you are looking for some extra cleanliess, here are 3 methods to clean coverslips:
Fast and easy but not great
Cleaning coverslip with 100% ethanol can help, flaming them would be even better. While that method does not give the best results, it can already help with a batch of coverslips that may not be of the best quality.
Fast, easy, and great but need the instrument
Plasma cleaning is another method to clean coverslip. It works very well and very easy to do.
Long and not easy but great
Base piranha cleaning is also a great method to clean coverslip. But a dangerous one too. People should be trained to avoid any serious injuries.
The following protocol is a very thorough type of cleaning:
1% Hellmanex III (Fisher Scientific, Hampton, NH) for 3 h at 25°C, rinsed with distilled water, and placed in acetone at 70°C for 10 min. This was followed by a secondary cleaning with a mixture of 1:1:5 (vol/vol) of hydrogen peroxide (30%):ammonium hydroxide:water for 1 h at 70°C. Coverslips were rinsed in distilled water and stored in 100% ethanol.