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Add your microscopes and detectors

Register a microscope to the SmartScope database

Now that the connection to SerialEM works, we can add our microscope to the database.

To do so, navigate to the admin portal and then the Microscopes section and add microscope. It should bring you to localhost:48000/admin/detector/add/.

Then follow the instructions on how to add a microscope

Register a detector to the SmartScope database

Warning

Each microscope must have least one detector.

Similarly to adding a microscope, navigate to the admin portal and then the Detectors section and add. It should bring you to localhost:48000/admin/detector/add/.

Then follow the instructions on how to add a detector

Steps specific to JEOL CRYO ARM systems

To run SmartScope on CRYO ARM a few options need to be enabled in the microscope tab since all the scopes have the following items:

  • Aperture Control
  • Cold FEG
  • Energy Filter (for every detector entry)

To manage grid exchanges, the LongOperation In command should be used everytime the contents of the specporter changes. When creating sessions, the SerialEM grid ID from the first column of the command output should be used.

All the imaging steps will be executed in Low Dose Mode. The Atlas and Square mags a both going to use Search. The default settings for Search should be the Square mag. The atlas mag must be save as a Search imaging state with the name Atlas. SmartScope will call the Atlas state during atlas imaging and restore the previous state after acquisition.