Gatan K2 installation and setup » History » Revision 39
Revision 38 (Anchi Cheng, 08/14/2018 08:42 PM) → Revision 39/47 (Anchi Cheng, 08/21/2018 03:11 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 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 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. [[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.
* *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 This reduces idle time for the frame alignment scope, but it may cause memory leak in Appion. With the speed of frame alignment, super-resolution mode See Issue #3750 for update on this is more and more acceptable.
feature.
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]]