When you have set up and positioned one or several overview images (OVs) and one or several grids, you can click on the “Start” button in the Main Controls window to start the acquisition. Make sure that you have switched on and focused the beam. You can review several critical settings in a dialog that will pop up before you confirm the start of the acquisition. If the option ‘Take overviews’ is activated, you will be asked to confirm that the first OV is free from debris.

The current status of an acquisition is shown in the ‘acquisition panel’ in the Main Controls windows. Here you can activate and deactivate a number of options: e-mail monitoring, overviews, debris detection, Ask User mode, disk mirroring, image monitoring, auto focus (or focus tracking) and (if installed) plasma cleaning. On the right, you can see current estimates for the duration of the stack as well as the electron dose range (lower value for overviews, higher value for tiles) and the stack’s dimensions.

Acquisition panel in the Main Controls window

While an acquisition is running, you can use the Viewport to monitor it: Selecting “Show tile previews” in the control panel of the Viewport will show you downsampled images of the most recently acquired tiles at the positions in the grids where they were acquired. In the Slice-by-slice viewer, you can inspect a selected tile or overview images in successive slices.

Click on the “Pause” button in Main Controls to pause an acquisition. A dialog will pop up, in which you need to specify how you want to pause the acquisition. You can either pause immediately (acquisition will pause after completing the acquisition of the current image) or after finishing the current slice.


This part of the user guide is under development.