TIRF alignment guide

Aligning TIRF:

Setting up the microscope to prepare for TIRF alignment

1) Bertrand lens switch: Rotate to "B" (counterclockwise) - will need to adjust small rotatory button on this switch in a later step 2) Change side switch: From Eye -> Camera (rotate) (on the right of the microscope, under the eye pieces) 3) Switch Box-lights on (proximity sensor button top right of big incubator box on microscope) 4) Change Observation mode: Camera L + Eyes (bottom button out of 4 round buttons, front of the microscope) 5) Move Condenser down (inside black box, above sample) as low as reasonably possible (not hitting the sample...) by adjusting one of the rotary buttons on either side of condenser

Placing the sample and finding it

1) Select the lens (e.g. 100X) 2) Lower the lens with ESC, hold ESC to make that the current position 3) Put oil on the lens 4) Center the sample holder 5) Place the sample on the holder 6) Switch on an illumination mode (e.g. brightfield, or epifluorescence in the software) 7) Find focus on the sample (lens up until image = sharp) 8) (optional) switch on PFS to keep this focus

TIRF alignment in the software

1) Select TIRF Prime BSI mode, pick an OC to be aligned 2) Go "LiveAllCameras" and select the Fi3 view window 3) Press "Eyes only" on the front of the microscope (top button / observation method) 4) Using the Fi3 window (should probably adjust brightness/contrast of this view, done in the LUTs window), align the laser belonging to the desired OC you are configuring (step 5) 5) In the Ti2 E-TIRF Pad, hit Align and give it the correct fully reflecting critical angle for about 5-6 different rotations 6) Press "compute zeo from critical angles" and close window with "OK" 7) (optional) move on to another Optical Configuration, and repeat steps 1-6 for that particular laser