Leginon

h1. Falcon Orius combo installation and setup

h1. Falcon/Orius combo unique installation and setup

h2. Falcon/Orius is controlled by the same computer as the microscope

Currently working configuration uses TIA and TIA Scripting to control Falcon and Gatan Digital Micrograph Scripting to control Orius.

h2. Extra Package and Installation

* Use all 32-bit version of Windows installer

|_.program/package|_.notes|

|TecnaiCCD.dll |(Should come with the microscope).|

|Tia.dll |(Should come with the microscope)|

{{include(comtypes installer)}}

h3. Register TecnaiCCD.dll  (It may have been registered already)

*  From the command prompt, run the following commands.  You may need to enter the full path of the dll:

<pre>REGSVR32 TecnaiCCD.dll</pre>

h3. Run updatecom.py

* From a command line window:

<pre>cd C:\python27\Lib\site-packages\pyscope

C:\python27\python.exe updatecom.py</pre>

* The output sould contain this output for DM scripting

<pre>

initializing Gatan CCD Camera done.

</pre>

and one of these outputs for TIA scripting

<pre>

initializing ES Vision 3.0 done.

initializing ES Vision 3.1 done.

</pre>

h2. instruments.cfg

{{include(Instrumentscfg_for_falcon_orius)}}

h2. Setup

* 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.

* 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. Testing with pyscope

h3. Testing Orius

<pre>

from pyscope import tia

g = gatan.Gatan()

g.setExposureTime(100)

g.getImage()

</pre>

h3. Testing Falcon

<pre>

from pyscope import tia

g = tia.TIA_Falcon()

g.setExposureTime(1000)

g.getImage()

</pre>

h2. Programs to open before Leginon Client: Digital Micrograph and then TIA