The Elyra is equipped with a levelling stage insert. There are instructions for levelling the stage on the desktop of the computer. Please do not do it yourself unless you have been trained by facility staff. The levelling feature is important for both SIM and TIRF. However, due to the shape of the insert, certain sample vessels are not suitable. The zeiss sample prep guide has complete instructions, however, there are a few additional points to note below.
We recommend high precision 18mm x 18mm coverslips, mounted in the centre of the slide (the whole slide, not just the unfrosted section). In the image below, a 22mm x 2mm coverslip has been used. One corner of the coverslip is resting on the 'arm' of the insert and this causes the coverslip to not be level to the image plane. This defeats the purpose of having a levelling stage, and it is for this reason that we recommend you use only 1 coverslip per slide, mounted in the middle, and the coverslip should be 18mm or smaller in width or diameter. We also do not recommend the common practice of trying to fit as many coverslips as possible onto the slide, as this may cause the slide to not rest level as well.
If you wish to use chambered coverslips, we recommend the 2 or 4 chambered ones. the 8-chambered ones are impossible to image with the high NA objectives as the objective has to get too close to the 'arms' of the stage insert as well. This causes huge amounts of frustration to users, and potential damage to the objectives. You will not be able to image the whole surface area of your chambers. The middle 'aisle' of the slide is about the best that we can manage with this sample holder. TIRF may not work with chambered coverslips.