Last updated on 9/20/19
5
10. Adjust preset intensity - this should be checked for every square used for imaging as
stain thickness varies
a. Send sq preset to scope
b. With the flu screen down, adjust current density (on monitor) to be between 20
and 25 pA/cm2 using the brightness knob on the control panel
*note: if you cannot see beam, lower mag and adjust beam shift first
c. In Leginon, click “edit selected preset parameters”, and click the icon “import
from scope” for intensity and save
d. Repeat for hl, fa, fc, and en (any high mag changes can be adjusted using one
preset and )
11. Adjust high mag beam shift
a. Send en preset to scope
b. With beam shift selected on the control panel, right click and drag the mouse to
center beam
c. Through leginon, click “edit selected preset parameters”, and click the icon
“import from scope” for beam shift and save
i. You can also import the beam shift for fa and fc presets
ii. Note: you may need to adjust beam intensity after shifting the beam.
d. Lift screen (close the furthest left panel on the scope monitor; click “screen” to
lift/lower flu screen)
12. Simulate square target
a. In the J1Square node…
b. Click simulate target (+++)
13. Submit subsquare targets
a. In the J1Subsquare_Targeting node…
b. Use the acquisition mouse pointer to select subsquare area of interest
c. Use the focus mouse to select eucentric height target
d. Click “Submit Targets”
e. Click “Submit Queued Targets”
f. At this point, you should see action happening in the J1Z_Focus node and
J1Subsquare node
14. Submit exposure targets
a. In the J1Exposure_Targeting node...
b. Use the acquisition mouse pointer to select exposure targets
c. Use the focus mouse to select eucentric focus target
d. Click “Submit Targets”
e. You should see action in the Drift_Manager, J1Focus and J1Exposure nodes
15. Repeat steps 7 - 10 until you are done collecting data
16. End of session:
a. Beam off
b. Send scope to en preset (SA MAG x60k)
c. Fluorescent screen down
d. Objective aperture out
e. Recenter stage
