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

h2. SEMCCD Digital Micrograph plug-in installation

{{include(Install_SerialEM_DigitalMicrograph_plugin)}}

h2. instruments.cfg

* A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template".  Copy it to

 <pre>C:\Program Files\myami\instruments.cfg</pre>

* Remove SimCam modules in the configuration.

{{include(Gatan_K2_Instruments_cfg)}}

h2. Setup

{{include(dm_camera_configuration)}}

* 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 dmsem.cfg.  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. [[older k2 dmsem configuration]]

h2. 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 and RAW_FRAME_DIR.  In addition, the path separator should be "\"

* *CAMERA_ID* is usually 0.  In the older version, it is defined in the same name below

<pre>

class GatanK2Base(DMSEM):

</pre>

h3. Early return

Early return speeds up data collection by allowing other processes to proceed until it needs to save another frame movie.  To turn this on, you set these values.  It only affects frame saving images.

* *DO_EARLY_RETURN = True*

* *EARLY_RETURN_FRAME_COUNT = 1*  This specifies the number of frames you want to integrate and return to you before all frames are saved. Typically people use 1 so that they still have some idea of the intensity.

The result of using this is that the image found in myamiweb (the integrated image of what you specified as EARLY_RETURN_FRAME_COUNT  is not meaningful until you align them through the frame alignment in Appion.  With the speed of frame alignment, this is more and more acceptable.

h3.  Saving frame movies as LZW compressed TIFF

* *SAVE_LZW_TIFF_FRAMES = True* makes it save in compressed tiff file.

h2. Testing with pyscope

{{include(Gatan_K2_Installation_Pyscope_Test)}}

h2. Trouble shooting

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 2.  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

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