Session page

The run session page offers control over the automated SmartScope workflow as well as the logging information.


Top section

  • Session name

  • Go to session browser: Redirect to the browser where the reports can be viewed.

  • Hard drive monitor: Provides basic information about the status of the hard drive capacity.

  • Process information: Provides basic information about the status of the session

Control buttons


This is the main button to start and stop a run.


The stop button will issue a soft stop signal and the run could take a few minutes to stop. Essentially, SmartScope will finish the current acquisition and stop when it queries the next item in the queue.

Pause between grid

This toggle button with enable (green) or disable (red) an optinal prompt to pause before moving to the next grid. The goal is to allow users to verify the results and make sure they’re satisfactory before moving to the next sample.

Admin control buttons

These buttons will only appear when logged in as a staff user

Force start

In some cases, main due to errors and crashed, the process may not have cleaned up properly, resulting in the stop button not reverting to start. This button serves as an override to re-start the session.

Remove scope lock file

When a run is started on a given microscope, a lock file is written to the file system. This prevents a second run to be started simultaneously, which would result in a crash. Again, in some error cases, the lock file may not get automatically removed. This button will force it’s removal


When a run is started with a lock file present. A message will appear in the log that the microscope is locked and the process will terminate before iniating a connection to the microscope.

Force-kill all session processes

Unlike the stop button, this button will immediately kill the SmartScope process and disconnect from the microscope. Use in case of emergency.


This will probably results in not cleaning up the lock file or udpating the process status correctly. It is likely that the other 2 buttons will need to be used to restart.


Pressing this button is better than using the stop button in SerialEM. However in case of major emergency, pressing the stop button will immediately break the connection between SmartScope and SerialEM. However, SerialEM will need to be closed and restarted to allow a reconnection.


At the bottom of the page, there are 3 log panels. The top one displays the current items in the queue for imaging, the middle one follows the imaging process and the last one follows the image processing process.

Pop-up notifications

There are multiple messages that may show up in the top sections during the run. Here’s a list of them.

Scope lock warnings

Notifies that the microscope bound to the session is currently being used. If the session that controls the lock is the one on the current page, a link to navigate to the current session with appear.

Stop signal received

After presseing the stop button, it notifies that the stop signal has been received and that the process will end after the current acquisition or set of acquisisions.

Pause between grid prompt

This prompt appears when the screening is finished on the current grid and the Pause between grid is enabled. The pop-up contains 2 buttons. On to continue the current grid and one to proceed to the next grid.


Before selecting Continue to next grid, more targets will need to be added to the queue. Otherwise, the prompt will immediately reappear without doing anything.