Gatan on Windows with semccddll » History » Revision 4
Revision 3 (Anchi Cheng, 02/02/2016 02:07 PM) → Revision 4/11 (Anchi Cheng, 02/02/2016 02:12 PM)
h1. Gatan on Windows-32 with SEMCCD.dll
dmsem module uses SEMCCD.dll written for SerialEM to communicate with Gatan software rather than tecnaiccd.dll
If using this on a computer different from the scope computer, please read [[Using_Leginon_on_a_system_where_the_microscope_and_camera_are_controlled_by_different_computers|this]] first.
h2. Extra Package and Installation
* Use all win32 version of Windows installer
* SerialEM DigitalMicrograph Plug-in
{{include(Install_SerialEM_DigitalMicrograph_plugin)}}
h2. instruments.cfg
Currently UltraScan and Orius camera are supported.
For UltraScan camera (US4000), set instruments.cfg to use GatanUltraScan class. For example:
<pre>
[us4000]
class: dmsem.GatanUltraScan
zplane: 50
height: 4096
width: 4096
</pre>
h2. Setup
{{include(dm [[dm camera configuration)}} configuration]]
!camera_configuration.png!
* Set camera configuration to give the [[Leginon Image Orientation|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 [[Low_dose_shutter_configuration_for_Gatan_camera_in_Digital_Micrograph_program|shutter configuration in DM]] to protect the specimen when camera is not taking images.
h2. (Version 3.2) Define local configuration in dmsem.cfg
# Copy from your myami checkout pyscope/dmsem.cfg.template to C:\Program Files\myami\dmsem.cfg
# 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:
<pre>
[dm]
DM_VERSION = 2.32.788.0
[ultrascan]
CAMERA_ID = 0
FLIP = True
ROTATE = 0
</pre>
h2. Testing with pyscope
[[Gatan UltraScan dmsem Installation Pyscope Test]]
{{include(Gatan_UltraScan_dmsem_Installation_Pyscope_Test)}}
h2. Trouble shooting
h3. Refused socket connection
If an error of "No connection could be made because the target machine actively refused it" comes up in the above test.
If not blocked by firewall, the SERIALEM_CCD_PORT specified in environment variable may be locked by a remaining previous attempt.
You can check active tcp port with Windows command
<pre>
netstat
</pre>
* In some case, you will find SERIALEMCCD or similar listed in Windows Task Manager Processing list. If so, and that process remains after Digital Micrograph is closed, you can terminate it from Task Manager.
* CurrPorts is a program that can be used to check and close socket tcp connection with gui.
h3. SerialEM-CCD plugin can output the command it issues and results to DM's result panel if you set the environment variable SERIALEMCCD_DEBUG to larger than 0. Set to 1 to show general log. Set to 2 to also include socket communication log. Please activate this debug log and include the portion that shows problem when reporting problems to Leginon team.
h2. Programs to open before Leginon Client: Digital Micrograph