Differences

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--- glacios_screening [2023/01/16 14:01] – [6. Prepare Serial-EM for screening] marechan
+++ glacios_screening [2023/11/01 20:18] (current) – external edit 127.0.0.1
@@ Line 4: / Line 4: @@
-==== 1. Load the Grids ====
+==== 1. Load  Grid ====
   - ++Introduce your grids in the cassette|<div>
@@ Line 13: / Line 13: @@
   - ++Check Autoloder temperatures, then load the NanoCab in the microscope|<div>{{ :autoloader_tempertures_all.png?nolink |}}
 </div>++
-  - Remove the NanoCab
@@ Line 33: / Line 36: @@
 </div>++
   - ++Load platform or user settings|<div>
-  * Menu: //Settings > Open > SerialEM_Settings_SPA//
+  * Menu: //Settings > Open > Platform_Settings_SPA//
 </div>++
@@ Line 100: / Line 103: @@
     * On the microscope computer, make sure beam settings were updated according to Atlas imaging state.
 </div>++
+  - Open the column valves.
   - ++(Optional) Determine the overall eucentric height.|<div>
     * In Serial-EM, center a square in the middle of the grid.
       - add a marker (green cross) by **left-clicking** on a square.
       - in the navigator **windows** press the //go to marker// button. Wait for the stage to reach the specified position.
-      - take a //record// image.
+      - take a //record// image.{{ :camera_and_script_panel_record.png?nolink&400 |}}
       - if the square is off-center: keep pressed the right mouse button, grab the center of the square to the center of the screen, and release the button. Wait for the stage to reach its position.
      * In //Tasks// **tab** > //Eucentricity// > press on //Rough Eucentricity//.
@@ Line 192: / Line 196: @@
     * If you did a mistake, like applying the shift with an atlas/square map selected instead of the point, the sift can be deleted in Navigator **tab** > //Undo last Shift//.
 </div>++
+  - Correct for coordinate discrepancy between View and Record Magnifications.
   - ++Select the focusing area|<div>
   - Center a hole. If you plan to record images at the hole periphery, center the camera closer to a hole edge.
@@ Line 232: / Line 237: @@
   - In the //Low Dose Control// panel, tick //Continuous Update//.
   - Switch to **record beam** with the //Rec.// button.
+  - On the console, press the **Eucentric Focus** button.
   - Lower the fluorescent screen.
   - In TEM User Interface > //Tune or Autoloader// tab > //Direct Alignments// panel: press on **beam shift**.
   - With **multifunction X & Y knobs**, center the beam on the fluorescent screen, then press //Done//.
   - Switch to **View beam** with the //Vie.// button. Tick //Set// in //Additional beam shift//. **View beam only need to be centered once**.
-  - With the **trackball**, center the view beam on the fluorescent screen.
+  - With the **trackball**, center the view beam on the fluorescent screen. **Untick** the //Set// button.
   - Center the Record beam again as described above.
   - Switch to **Focus beam** (//Foc.// button) and change its diameter with the intensity knob according with the desired focus surface (depends on your hole spacing).
   - Center focus beam as explained for the view beam (with //Set// ticked and trackball).
   - Switch to **Trial beam** (//Tri.// button) and change its diameter with the intensity. Trial beam will be used for auto-centering and its diameter should fit in the camera field (green square) on the fluorescent screen.
-  - Repeat Record (Beam Shift + M X/Y), Focus and Trial (//Set// ticked + Trackball) until all beams stay centered.
+  - Repeat Record (Beam Shift + M X/Y), Focus and Trial (//Set// ticked + Trackball) centering until all beams stay centered.
+  - Untick //Continuous update// on the //Low Dose Control// panel.
 </div>++
   - In an empty hole or a broken square: Menu > Scripts > run > DatasetDefineVacuumIntensity