Gatan on Windows-32 with dmsem¶

dmsem module uses SEMCCD from distributed by SerialEM to communicate with Gatan software rather than tecnaiccd.dll

If using this on a computer different from the scope computer, please read this first.

Extra Package and Installation¶

• Use all win32 version of Windows installer

• SerialEM DigitalMicrograph Plug-in

Thanks to David Mastronarde for providing his DM plug-in using socket connection

Note: If you have SerialEM installed on the same computer, you don't have to go through this. The same Plugin can be used by both programs and share the same port¶

Remove your older SEMCCDxxxx.dll in C:\Program File\Gatan\Plugins if you had it from prevous leginon-only installtion¶

Download and extract the files¶

1. From your browser, go to [[ https://bio3d.colorado.edu/ftp/SerialEM/FrameAlignment/]]
2. Choose Shrmemframe*..exe for your version of DM to download to your Gatan PC.
3. Run the downloaded file and follow its instructions.

Add a new environment variable SERIALEMCCD_PORT if not exist already from SerialEM installation. Set the value to an unused port between 50000 and 60000 to avoid conflict with other programs. Avoid ports used by Leginon, especially not 55555.

Port 50000 or 50001 usually works.

instruments.cfg¶

Currently UltraScan and Orius camera are supported.

For UltraScan camera (US4000), set instruments.cfg to use GatanUltraScan class. For example:

[us4000]
class: dmsem.GatanUltraScan
zplane: 50
height: 4096
width: 4096

Setup¶

• Set camera configuration to give the standard Leginon orientation. For example, we need flip around the vertical axis on FEI T12. Note that the rotation required is different if it is installed post-GIF and/or on Krios.
• Set the shutter configuration in DM to protect the specimen when camera is not taking images.

(Version 3.2) Define local configuration in dmsem.cfg¶

1. Copy from your myami checkout pyscope/dmsem.cfg.template to C:\Program Files\myami\dmsem.cfg
2. Make changes to the configured value in dmsem.cfg

Most parameters are explained above.

• The config parser takes "'" and "\" literally. Therefore, do not include "'" in DM_VERION. In addition, the path separator should be "\"
• CAMERA_ID is usually 0 if it is the only Gatan camera.
• *Ultrascan camera should be configured under utrascan module, and Orius camera should be configured under orius module.

For example, only UltraScan camera exists on this computer that has Digital Micrograph version 2.32.788.0, and DM camera configuration
has vertical flip but no rotation, then set the dmsem.cfg ultrascan module like this:

[dm]
DM_VERSION = 2.32.788.0

[ultrascan]
CAMERA_ID = 0
FLIP = True
ROTATE = 0