Flow Control

Start and Stop Acquisition

After you configure the spectrum image (SI) acquisition parameters and any artifact corrections, click Capture on the STEM SI palette to start the acquisition.
 

If you want to refresh the survey image before starting:

1. Right‑click the survey image.
2. Select Restart Scan from the context menu.

Once the acquisition starts:

• The SI routine takes control of the microscope beam.
• The Capture button pulses blue, indicating that acquisition is active.
• Clicking the pulsing Capture button stops the acquisition.

A new workspace opens automatically and contains:

• A copy of the survey image
• Data containers for all acquired signals

Note: During an active SI acquisition, the spectrometers are unavailable for single‑spectrum acquisition.

Monitoring acquisition progress

If spatial drift correction is enabled, the system performs preliminary measurements before data acquisition. Depending on your preferences, visual feedback may be displayed.
 

While acquisition is running:

• Each SI appears in a new image window and fills progressively as data is acquired.
• Live spectra can be shown or hidden as needed.

To stop the acquisition at any time, click the pulsing Capture button.
 

When the acquisition is stopped or completed:

• Beam control returns to the Beam Safe Point, if configured.
• Otherwise, control returns to the microscope.

Pause and resume acquisition

During SI acquisition, you may need to adjust the microscope in a way that temporarily degrades spectrometer data. In these cases, pause the acquisition before making adjustments.

Pause the acquisition

• Click the pulsing Capture button while holding the Alt key.

The button label changes to Resume, indicating the acquisition is paused.
 

While paused:

• The beam moves to the Beam Safe Point, if defined.
• Otherwise, beam control returns to the microscope.

If Apply on Resume from Pause is enabled, spatial drift correction is performed automatically when acquisition resumes, before data collection continues.

Resume or stop from paused state

• To resume acquisition, click Resume.
• To stop acquisition, click Resume while holding the Alt key.

Note: Pausing is not available for hardware-synchronized acquisitions. On systems that, by default, use hardware-synchronized acquisition, you can force software synchronization via the Setup dialog.

After the acquisition

After acquisition completes:

• If Autosave is enabled, all experimental data is saved immediately using the current SI group saving options.
• If Close column valves after acquisition is enabled, the microscope column valves close automatically (on supported systems).

The survey image remains active in the View workspace, allowing you to quickly restart an identical or similar acquisition after adjusting survey ROIs or parameters.