Flow control


Once the spectrum image (SI) acquisition parameters and any artifact corrections have been set up, to start an acquisition hit the Capture button on the STEM-SI palette. If you wish to update the survey image before proceeding with acquisition, right click on it and select Restart scan from the context menu.

Once started, the SI acquisition routine will take control of the microscope beam, and acquisition will then begin. During acquisition, the Capture button will pulse in blue indicating that an acquisition is active and that a subsequent click of this button will halt acquisition. A new workspace is created and filled with a copy of the survey image and data containers for all acquired signals.

Note: During active SI acquisition, the spectrometers being used will not be available for single spectrum acquisition.

If spatial drift correction is enabled, then some preliminary measurements will be performed. Visual feedback on the measurements may be provided, depending on the preferences specified.

You can monitor how the acquisition is proceeding using the Visual Feedback provided. Each SI will be displayed as a new image window, which will fill as the acquisition proceeds. Live spectra may also be shown or hidden as desired. If at any point you wish to halt the acquisition, click on the pulsing Capture button. When the acquisition is halted or completes, the beam control is returned to the Beam Safe Point if one has been set up, or alternatively it is returned to the microscope.


During a SI acquisition, it may become necessary to perform a microscope adjustment that will temporarily degrade the data being collected by the spectrometer. At such times, you should pause the acquisition, carry out the adjustment, and resume after conditions have stabilized. To pause the acquisition at any time, click on the pulsing Capture button in the STEM-SI palette while keeping the Alt key pressed at the same time. The label of the Capture button changes to Resume.

When the acquisition is paused, the beam is either moved to the beam Safe Point if you have defined one, or otherwise beam control is returned to the microscope. If the acquisition is paused and restarted, the software immediately carries out spatial drift corrections if Apply on Resume from Pause has been enabled, before continuing to acquire data from where it was before the pause.

To resume acquisition from paused state, click on the Resume button. To stop acquisition from paused state, click on the Resume button while keeping the Alt key pressed at the same time.

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

After the acquisition

If the auto save functionality is enabled, all experimental data as saved immediately using the current SI group saving options. If the close column values after acquisition option is enabled, the microscope column valves are closed (on systems which support column valve access). You can use the (still) active survey image on the View workspace to immediately restart an identical or similar acquisition after adjusting survey ROIs and parameters.