Some STM manufacturers propose variable temperature STMs in which the sample is cooled but the tip is not. It is easy to monitor the overall sample temperature, but given that the tip is very close to the sample and at RT, the tip will certainly heat the tunnelling junction area. Would this temperature increase be significant (more than say 5 Kelvin)?
Are you talking about He cooled STM ? Such a STM head is enclosed in a cryostat, and all the parts of it are at a similar temperature.
I know that issue with nitrogen cooled STM where the STM head is not enclosed in a cryostat. In that situation, no noticeable heating of the sample by the tip. The main drawback is that tip and sample are not at thermal equilibrium, which can be annoying or unacceptable if you want to perform spectroscopy. You may also encounter severe thermal drift in such a microscope.
If your sample is facing directly a 300 K environment and its radiation, you can be almost sure it is significantly hotter than 5K. The best way to test local temperature is to perform a tunnel spectroscopy and extract temperature from thermal broadening.
if it a perfectly low temperature, that means both the tip-sample are cooled, then the junction temperature should be same as the sample. But if you are using variable temperature STM, then only sample is cooled. Tip is always at room temperature. Thus the junction temperature is not equal to sample temperature. One needs to be careful while mentioning the temperature. It is neither helium temperature, nor 300K. There was a study done and published in PRL about this. check this for example Phys. Rev. Lett. 105, 166101.
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