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Assuming the correct condenser is installed, place your sample on the microscope sample stage over a hole (the black three-holed microscope slides will work for this purpose, or any other holder you have that allows light to pass through the sample). If the sample is transparent to the eye then you can use it to align for transmission mode. If not, place your sample over one hole, and make sure there is another hole available on the sample stage for aligning. Adjust the focus such that the sample is directly below one of the upper microscope objectives and focus on the top surface of your sample, as described in the Reflection measurement setup above.
Once the sample is in focus, adjust the condenser focus to collect the transmitted light from the same location where the upper objective is focusing the incoming light. Move the stage to a hole and select transmission mode with the black button on the lower front of the microscope. Turn on the aperture illumination using the knob located furthest from you at the base of the microscope on the left hand side. Adjust the condenser height (red-labeled knob, base of microscope, right hand side) until aperture image is in focus (it should look like a square with sharp edges). Once the aperture image is in focus, center the aperture on the crosshairs by repositioning the condenser. These adjusters are not very linear and it takes some playing to get used to the way they move the lower aperture. You can tweak the position of the condenser while looking at the IR signal (Collect >> Experimental Setup >> Bench tab) to optimize the signal.
Return the stage to your sample and proceed to the OMNIC section for software control.
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