Setup positions

• Find targets for acquisition in grid square or lamellae maps.
  
• Take your time and make the right choices here!
• Possible strategy: select everything that you think is ok, then revisit all a few times to be sure.
• We expect to be in properly setup Low Dose mode.

Find positions

Gatan PC

• Take a Low Dose View image, save it and make it a map, make sure to use bin 4 to save time later!
  
• Change the label to 'viewmap'.
  
• Take a Low Dose Preview image, save it and make it a map, make sure to use bin 4 to save time later!
• Change the label to 'previewmap'.
• Save the Navigator, it should look like this:
  
  
• Close the navigator.
  

Support PC

• Open SerialEM from the "DUMMY SerialEM - shortcut" on the Support pc Desktop.
  
• Open the navigator file.
• Save as with a different name, just to be safe.
  
• Find and select points.
• Make all points Acquisition points (A).
  
  
• Save the navigator file.

• SerialEM menu, Tools, select Virtual Anchor Maps.
• This takes some time depening on the amount of positions. A command window will open to show progress, it will automatically close when done:
  
• Close the navigator and SerialEM.

Gatan PC

• In SerialEM, open the new navigator file named xxx_automaps.nav.
• V_xxxx are the View maps, P_xxxx  are the Preview maps. The preview maps are set as Acquisition Points.
  

• Deselect all A points, select first V_xxxx map, select Collapse, click A twice, deselect Collapse:
  
  

• In the Navigator window, select the first V_xxxx position, click Shift + T.
  
  Now select the very last View map, click Shift + T again.
  
  

• Choose Single frame images:
  

• Don't change anything:
  
  
  
• Save as TS_001.mrc (as an example), click save.

• Setup the tilt series controler, click here for some ideas first, focus doesn't matter as we set that during acquisition by a script. When done click Ok.
  
  
  

• Now all Preview maps are selected as TS (Tilt Series) with numbered file name TS_xxx.mrc:
  
  

Setting up the Focus/Trial positions

• Low Dose needs to be on.
  

• Double click the View map to load it.
  
• Select the Preview map in the Navigator list.
• Select Edit Focus in the Navigator window.
  
• Click in the loaded View map to set the Focus/Trial position for this tilt series.
  
• The Navigator item should have TSP set now, continue for all points.