Why do I see peaks in the graphs of the PhoxyCube Reader Software when I open the incubator door / take the plates out of the incubator?

There are different reasons:

• Temperature effect: The signal of the optical sensor, especially the oxygen sensor, depends on temperature. If you open the incubator, the temperature changes. A temperature drop leads to decreasing oxygen / pH signals and vice versa.
• Opening of the incubator door can lead to an upward peak in oxygen because ambient air enters the (usually CO2 containing) atmosphere of the incubator.
• CO2 atmosphere: Opening the incubator door leads to an upward pH peak because CO2 leaves the incubator. As the pH of the buffer for cell cultivation is regulated by the CO2 atmosphere in the incubator, this leads to a higher pH within the sample.