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JEOL 1230 Instructions
Specimen Insertion
- Flip toggle switch to "pump" (G)
- Line up pin on holder with goniometer(G)
- Insert specimen holder to first sample stop (marked line indicates correct depth)
- You will hear a click
- Orange light will go on
- Monitor Vacuum condition:
- Go to "FR Panel" "monitor" "vacuum conditions"
- When SPC value is <50 insert holder by turning the holder slowly clockwise 1/8 turn to the 1st stop
- Slowly allow the vacuum to pull the holder in
- Grasp holder firmly then turn the holder slowly clockwise 1/4 turn to 2nd stop
- Slowly allow the vacuum to pull the holder in
- Wait for green light to come on before turning on beam

Aquiring a Beam
- Open "HT" Menu (top left screen)
- Select beam "on" *Filament current should be around 70%
- Be patient, it takes about one minute for the beam to appear
Condenser Aperture Alignment
- At 5000x
- Use "Brightness" knob to condense beam on function box(F)
- press "Beam Shift" (F)
- Right click mouse button and drag the beam to central position
- Spread Beam (over clockwise) with "Brightness" knob (F)
- If it does not spread evenly, center with the condenser aperture x-y controls
- condense beam with "Brightness" (F)
- If beam is not centered, repeat
- The beam should expand/ contract concentrically around the beam centre as the brightness is adjusted
Objective Aperture Alignment
- Select Diffraction mode by pressing "Diffraction" (F)
- Set the camera length to 150cm
- Condense beam with "Brightness" (F)
- Focus beam with "Diff focus" (F)
- Insert objective aperture
- Center aperture with x-y controls
Z Height Adjustment
- On the menu, go to Monitor, then enter Lens condition sub-menu.
- By adjusting the focus, set the objective lens current to 4.7.
- Enter Z cont mode, then click AUTO to set specimen eucentric height.
Diffraction
- Select Diffraction button (F)
- Use Align Adjust for Diffraction shift
- PL Align
Low Dose
Specimen Removal
- Switch the beam is off
- Switch the toggle to "Air" (G)
- Monitor Vacuum condition:
- Go to "FR Panel" "monitor" "vacuum conditions"
- Pull out specimen holder to 1st stop
- Rotate anti-clockwise 1/4 turn
- Pull out the specimen holder to the 2nd stop
- Rotate anti-clockwise 1/8 turn
- Wait for the airlock "SPC" to vent
- Gently remove the specimen rod (G)
- If the use of force is necessary the SPC is not vented
SerialEM Operation
Startup
- Launch Digital Micrograph
- Launch Temserver20xx.exe
- Launch your copy of SerialEM
Montaging
- To do a low-mag montage, go to 100X or 80X, fully expand beam, take a test Record image to be sure images are OK
- Go to Navigator menu, choose to Open
- Go to Navigator menu, choose Setup Full Montage
- Choose to save all header info, save file as FILENAME.st
- Increase overlap percent to 20 (3X3 images for full montage at 100X)
- Click Start on montage menu
- Montage will begin. If it appears to get stuck, quickly toggle mags
- When done, click YES to make a new map
- Try checking and unchecking Treat as very sloppy montage -- sometimes it is better, sometimes worse
- Go to File menu, click close to close the file for writing (do not want to add to this file)
Alignment of Montages
- First map is registration 1
- Make a new montage, either at a different mag or at a different grid orientation
- Follow instructions above, but before you click start, CHANGE CURRENT REGISTRATION TO 2
- Make the new map -- you now have old map in registration 1 and new in registration 2
- Need at least 3 points to align the maps (determine a shift/rotation matrix)
- Choose three obvious points, click Add Points, and add points. When done, click stop
- Mark each point as a Registration point, numbered 1, 2 and 3
- Re-open first map by double clicking
- CHANGE CURRENT REGISTRATION BACK TO 1
- Click Add Points, and add the three corresponding points on the old map
- Mark these as Registration Points , again 1,2,3, IN THE SAME ORDER AS ON MAP 2
- Change current registration back to 2, and re-load new map
- Under Navigator menu, choose Transform items
- Map 1 is now transformed onto map 2
Acquiring many areas using polygon montage
- Change to desired new magnification (say 4000X )
- Take Record image to test beam and image settings
- In low mag map, choose Add Polygon and outline a grid square
- With Polygon highlighted, go to Navigator menu and choose Setup Polygon Montage
- Increase overlap to 15%-20%, and also choose to Move Stage
- Change current registration as described above, and click start
- When polygon montage is done, create a new map and align it to old map as described above
- DO NOT CLOSE THE NEW FILE
- In low mag map, decide which squares are to be acquired, and add a point in the middle of each
- Mark each new point as ACQUIRE
- Under Navigator menu, choose Acquire Areas
- A polygon montage, centered at each point, will now be acquired.
Running a script at many points
- Under Macro mwnu, edit your script as desired
- In a map, choose to add points, and add them to desired areas
- Mark each point as ACQUIRE
- Under Navigator menu, choose Run Macro at areas
* Set ALLOWTOPICVIEW =
-- KdDerr - 13 Jun 2006
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