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Gatan K2 installation and setup » History » Revision 12

Revision 11 (Anchi Cheng, 05/27/2014 05:03 PM) → Revision 12/47 (Anchi Cheng, 06/05/2014 10:54 PM)

h1. Gatan K2 unique installation and setup 

 h2. Gatan K2 is controlled by a computer separated from the microscope 

 Please read [[Using_Leginon_on_a_system_where_the_microscope_and_camera_are_controlled_by_different_computers]] first. 

 h2. Extra Package and Installation 

 * Use all amd64 version of Windows installer 

 * SerialEM "SerialEM DigitalMicrograph Plug-in Plug-in":http://emg.nysbc.org/attachments/download/1817/SEMCCD-GMS2-64.dll 
 {{include(Install_SerialEM_DigitalMicrograph_plugin)}} 

 h2. instruments.cfg 

 {{include(Gatan_K2_Instruments_cfg)}} 

 h2. Setup 

 * Set camera configuration to 270 degree rotation and flip around the vertical axis to give the [[Leginon Image Orientation|standard Leginon orientation]].    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. 
 * Create the folder to store the dose fractionation raw frames.    Default location is D:\\frames. 
 * Setup [[DDD_raw_frame_file_transfer|raw frame file transfer]] from a network data server. 

 h2. Change Flag in pyscope/dmsem.py if you have DM 2.30 version and requires flip/rotation to give the Leginon orientation. 

 In standard python site-package installation, this file is at C:\Python27\Lib\site-packages\pyscope\demsem.py 

 Find this line near the top: 
 <pre> 
 isDM230 = False 
 </pre> 
 Change it to 
 <pre> 
 isDM230 = True 
 </pre> 

 h2. Testing with pyscope 

 {{include(Gatan_K2_Installation_Pyscope_Test)}} 

 h2. Programs to open before Leginon Client: Digital Micrograph 

 h2. See more about K2 implementation in [[Using_Gatan_K2_Summit_in_Leginon]]