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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)

Next, to manage grid exchanges, SerialEM must call the custom Transfer_Cartridge.bat script provided by JEOL. The default path for gridswapper is set to C:\Program Data\SerialEM\PyTool\Transfer_Cartridge.bat

If this path needs to be changed, a additional settings file must be created. First, find your microscope id from the url in the admin portal as show below:

Micropscope ID

Then create a file with MICROSCOPE_ID.yaml in shared/smartscope/

Then add the new path to the Transfer_Cartridge.bat as shown below:

transfer_cartridge_path: 'C:\PATH\TO\Transfer_Cartridge.bat'

Example on how to add it in a single command (please replace with your own values): 

echo "transfer_cartridge_path: 'C:\PATH\TO\Transfer_Cartridge.bat'" > shared/smartscope/7INHMHBe2LyOZ2xKEKpsAGhd889pCO.yaml