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--- glacios_collect [2022/02/11 14:35] – created bonnefon
+++ glacios_collect [2023/11/01 20:18] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-Setup an automated data collection at Glacios
+====== Setup an automated data collection at Glacios ======
-Beam microprobe and nanoprobe calibrations
-Introduce the Cross Grating Grid in the column.
+==== Beam microprobe and nanoprobe calibrations ====
-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.
+++++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**