Leginon

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 DigitalMicrograph Plug-in

{{include(Install_SerialEM_DigitalMicrograph_plugin)}}

h2. instruments.cfg

{{include(Gatan_K2_Instruments_cfg)}}

h2. Setup

!camera_configuration.png!

* Set camera configuration to give the [[Leginon Image Orientation|standard Leginon orientation]].  For example, we need 270 degree rotation and flip around the vertical axis on FEI F20.  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.

* K2 interface in DM restricts the exposure time to multiple of some set number, depending on the mode.  When you enter in DM an invalid number, it automatically change it to the valid one when you click the acquire button.  pyscope/dmsem.py has hard-coded values for these precision. Compare them to the precision of the DM version you have since it may change with DM version.

* K2 frame exposure time is adjustable in Leginon gui.  However, you need to check if the number is acceptable by DM using the above method.

* Create the folder to store the dose fractionation raw frames.  Frames are saved as unsigned 16-bit mrc image stack in K2 computer under D:\frames by default as set in the code inside pyscope/dmsem.py in the function calculateFileSavingParams.  You must create the frames directory first.  Leginon will not do that for you.  You may change where the frames are saved here but will need to make corresponding changes when setting up [[DDD_raw_frame_file_transfer|raw frame file transfer]]

* Setup [[DDD_raw_frame_file_transfer|raw frame file transfer]] from a network data server.

* Unless you want to develop your own frame alignment program.  We recommend that you [[appion:Direct_Detector_Frame_Processing|use Appion to do frame gain correction and alignment]].  These are parallelized by images so it cam almost keep up with the acquisition.

h2. (Version 3.0) 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\dmsem.py

Find this line near the top:

<pre>

isDM230 = False

</pre>

Change it to

<pre>

isDM230 = True

</pre>

h2. (Version 3.1) Define local configuration

h2. In C:\Python27\Lib\site-packages\pyscope/dmsem.py

<pre>

# DM Version

DM_VERSION = '2.30.542.0'

# the value in DM camera config

K2_CONFIG_FLIP = True

# multiple of 90 degrees (i.e. put 1 if 90 degrees, 3 if 270 degrees)

K2_CONFIG_ROTATE = 3

# raw frame base directory. Use '\\' as path separator

RAW_FRAME_DIR = 'D:\\frames\\'

</pre>

1. Find DM_Version in DM gui under its menu bar : /Help/About DigitalMicrograph

2. Fill in K2_CONFIG_FLIP and K2_CONFIG_ROTATE according to DM gui under its menu bar: /Camera/Configure Camera.  The comment line above the value setting explains the meaning of the value.

3. Enter the drive the directory where raw frames will be saved.

h2. (Version 3.2) Define local configuration in dmsem.cfg

copy from your myami checkout pyscope/dmsem.cfg.template to dmsem.cfg in the same directory.

Make change 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 and RAW_FRAME_DIR.  In addition, the path separator should be "\"

* *EARLY_RETURN_FRAME_COUNT* specifies the number of frames you want to integrate and return to you before all frames are saved.  This reduces idle time for the scope, but it may cause memory leak in super-resolution mode See Issue #3750 for update on this feature.

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]]