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External python setup

Setting up external python for SerialEM

Documentation on how to set up can be found on the SerialEM website. We have now installed on a few systems and here are some examples for setting up the SerialEMproperties.txt.

SocketServerIP 1 xxx.xxx.xxx.xxx, is the IP where the FEI-SEM-server.exe is running

Otherwise, SockerServerIP 7 should be the IP of the SerialEM PC.

Example: Talos Arctica with K2 or K3

  • Microscope PC IP: 192.168.0.3
  • Gatan PC IP: 192.168.0.32
  • SerialEM is installed on the Gatan PC

The following lines should be added to SerialEMproperties.txt. 

EnableExternalPython            1

It will enable the connection of SmartScope and other external python script to SerialEM at the SerialEM PC IP address (192.168.0.32 in the example above) on port 48888.

Tip

SerialEM needs to be restarted after changing properties.

Testing serialEM connection from SmartScope

To quickly test if your settings are good for the python connection to SerialEM, you can use the following commands and replace IP by the gatan PC address and port by 48888.

From our examples above, the Talos Arctica IP K2 PC is 192.168.0.32 and port would be 48888.

./smartscope.sh run test_serialem_connection IP port

Example

./smartscope.sh run test_serialem_connection 192.138.0.32 48888

docker exec smartscope smartscope.py test_serialem_connection IP port

Example

docker exec smartscope smartscope.py test_serialem_connection 192.138.0.32 48888

If the connection is successful, a Hello from smartscope message should appear in the SerialEM log window. Now, you can proceed to adding a microscope.