====== Setup an automated data collection at Glacios ======


==== Beam microprobe and nanoprobe calibrations ====

++++Prepare the Cross Grating grid for calibration|
  * Introduce the Cross Grating Grid in the column.
  * Go to x34 Imaging status.
  * Select 2 positions: a carbon square and an empty square.
  * Introduce the Condenser 2 of 30 um
  * Go to x280 Imaging status.
  * In DigitalMicrograph click View and place the mouse arrow on a feature.
  * Use Alpha Toogle 20° in Stage² window (TEM) to rock the grid.
  * Correct with **Z axis knobs** on the console.
  * Repeat a second time.
  * Go to x45k Imaging status
  * In Low Dose Control window (SEM) click on Go to: Record.
  * Push the **Eucentric Focus** knob on the console.
  * Inset the screen (FC).
  * Push the **Wobbler** knob on the console.
  * Adjust the Z height on the screen  with the **Z axis knobs** on the console.
++++

== Microprobe ==

Focus the beam and center it (with the trackball).

  * Go to microprobe (TEM)
  * Push the **Eucentric Focus** knob on the console.
  * In the **Direct Alignments** window: 
  - Adjust the ++Beam tilt pp X|<div>
  * Click on **Beam tilt pp X** 
  * Adjust with **Multifunction X/Y** knobs
  * Click **Done** at the bottom of the window.
</div>++
  - Adjust the ++Beam tilt pp Y|<div>
  * Click on **Beam tilt pp Y**.
  * Adjust with **Multifunction X/Y** knobs.
  * Click **Done** at the bottom of the window.
</div>++
  - Adjust the ++Beam shift|<div> 
  * Click on **Beam shift**.
  * Adjust with **Multifunction X/Y** knobs.
  * Click **Done** at the bottom of the window.
</div>++
  - Adjust the ++Rotation center|<div>
  * Click on **Rotation center**.
  * Adjust with **Multifunction X/Y** knobs.
  * Click **Done** at the bottom of the window.
</div>++

== Nanoprobe ==

Focus the beam and center it (with the trackball).

  * Go to nanoprobe (TEM)
  * Push the **Eucentric Focus** knob on the console.
  * Check the Condenser 2 centering and adjust if necessary.
  * In the **Direct Alignments** window: 
  - Adjust the ++Beam tilt pp X|<div>
  * Click on **Beam tilt pp X** 
  * Adjust with **Multifunction X/Y** knobs
  * Click **Done** at the bottom of the window
</div>++
  - Adjust the ++Beam tilt pp Y|<div>
  * Click on **Beam tilt pp Y**
  * Adjust with **Multifunction X/Y** knobs.
  * Click **Done** at the bottom of the window
</div>++
  - Adjust the ++Beam shift|<div> 
  * Click on **Beam shift**
  * Adjust with **Multifunction X/Y** knobs
  * Click **Done** at the bottom of the window
</div>++
  - Adjust the ++Rotation center|<div>
  * Click on **Rotation center**
  * Adjust with **Multifunction X/Y** knobs
  * Click **Done** at the bottom of the window
</div>++

++++After all calibrations save the settings|
  * Menu: //Settings > Save//
  * In **Low Dose Control** window check **Continuous update**
  * Click on Update it
  * Uncheck **Continuous update**
  * Menu: //Settings > Save//
++++

==== Correct astigmatism ====

  * Verify that the **Turbo Auto Off** Vacuum option is checked (TEM)
  * Go to x45k Imaging status
  * In the Camera and script window (SEM) open the **Setup**
  * In Record Tab, set 2 sec exposure, processing unnormalized, align frames, save frames and the objective diaphragm out
  * If the signal is too weak, increase the time, concentrate the beam or change the carbon area
  * ++Correct astigmatism by CTF|<div>
  * Menu: Calibration > Focus & Tuning > Correct astigmatism by CTF
  * Open FFT window with Shift+F
  * Repeat several times until the corrected parameters have converged
</div>++
  * ++Coma free align by CTF|<div>
  * Menu: Calibration > Focus & Tuning > Coma free align by CTF
  * Open FFT window with Shift+F
</div>++
  * ++Coma vs image shift|<div>
  * Menu: Calibration > Focus & Tuning > Coma vs image shift
  * Open FFT window with Shift+F
  * If the signal is too weak, increase the time, set binning, concentrate the beam or change the carbon area
  * parameters for R 1.2/1.3 grids: 5 μm
  * parameters for R 2/2 grids: 6 μm
</div>++

Introduce the Objective aperture and redo the Correct astigmatism by CTF step once.

----

==== Configuration of the multihole / multishot acquisition ====

Do this configuration just before starting the acquisition on one of the squares selected for the whole acquisition after correction of the image shift in x280 and LD mode imaging states.

  * On the square map, mark the positions of the 4 holes at the corners of a 9 holes square.
  * Go to the center hole with **Go to marker** and properly center on the hole with **Stage shift**.
  * Press View in LD mode (ensure that defocus is below -20)
  * Open Menu: //Navigation > Montaging & grids > Set multi//
  * Change the parameters of the multishot for calibration
  * Click on the central hole for positioning
  * Adjust the number of shots per hole (in general 3)
  * Adjust the distance (72 in general for R 2/2 grids)
  * Menu: //Navigation > Montaging & grids > Find hole in regul// to configure
  * Select regular pattern 3 x 3
  * ++Calibrate after ensuring proper centering on the center hole|<div>
  * Move by Image shift to the first corner
  * Center properly in the hole using zoom if necessary
  * Save the position by clicking on **Save image shift**
  * Proceed to the next corner and repeat
</div>++
  * Save the settings in //Menu > Settings > Save//

== Beam tuning ==

  * Ensure that LD modes View and Record are perfectly aligned
  * Calibrate the proper centering in Record/View/Focus/Trial modes
 
  * Precisely center Record beam with Direct Alignments/Beam shift
  * Check **Continuous update**
  * Press View and recenter if necessary with set add beam shift
  * ++Then cycle several times between the modes until the beam stop moving|<div>
  * Press **Record** and correct Direct Alignments/Beam shift
  * Press **Focus** and set add beam shift
  * Press **Trial** and set add beam shift
  * Repeat
</div>++
  * Uncheck **Continuous update**