Exchanging specimens

Schematics of the sample mounts can be found at http://xray1.physics.sunysb.edu/user/manuals.php .

We begin by assuming that the microscope is properly aligned and that all the alignment parameters were set up correctly when setting up the microscope. The procedure for exchanging a specimen is:

• Go to Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Retract specimen. This will retract ZDET downstream and ZSTG downstream by 2 mm to be able to safely exchange the sample. Note that the standard specimen mounting slot on the piezo stage prevents you from bumping the order sorting aperture (OSA), which is a nice feature.
• Exchange the specimen. For the inboard branch follow the instructions to vent the chamber (Sec. 3.3) first.
• Insert the VLM with Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Detector: Insert VLM.

• Open the window Alignment $\rightarrow$ Align and Focus Sample with VLM (also see Sec. 5.11). Observe the sample on the VLM and use the controls in the window which popped up to focus onto the sample (ZDET) and laterally move it to the desired position (XSTG, YSTG). If you are inserting the pinhole remember that you have to move the VLM about 100 $\mu$m farther upstream to compensate for the thickness of the pinhole foil.

  In principle you could also use the popup windows from the "Move" menu for the above. In this case, however, you must make sure to use ZDET (NOT ZSTG!) to get the VLM to focus on the specimen. The lateral position of the sample has to be changed with XSTG and YSTG (NOT XDET and YDET) because you need to adjust the specimen position relative to the beam!

• Once you have focused on the desired specimen area, hit Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Record Alignment $\rightarrow$ Record specimen in VLM focus to indicate to the computer is in the VLM focus.
• For the inboard branch follow the instructions in Sec. 3.2 to fill the chamber with Helium. During this process the positions of the sample may change a little, so repeat the previous step afterwards.
• Insert the specimen (Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Insert specimen)
• Insert the detector of your choice with Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Detector: Insert XY.
• Insert the specimen again (Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Insert specimen) to correct the distance between specimen and detector. The specimen should now be within about 20 $\mu$m of the correct focus position, thanks to the VLM prefocusing.
• Do an overview scan to check that you're on the desired sample area: Scan $\rightarrow$ Stepper
• Do a focus scan to optimize the x-ray focus on the specimen. When you have moved into x-ray focus, you must record it with Alignment $\rightarrow$ Edit Alignment $\rightarrow$ Record Alignment $\rightarrow$ Record specimen in X-ray focus. This will ensure that when you change the photon energy, your specimen will be moved accordingly into the new focus position. You may record the x-ray focus at any time (i.e., you can re-focus and re-record the focus later on for a different specimen area).
• Save the alignment with Alignment $\rightarrow$ Write Alignment File. You must do this if you want to exit SM_GUI and run sm_script to take a stack, for example!