Setup SerialEM for K2 on FEI Scope

Chen Xu

$BrandeisEM: emdoc-xml/en_US.ISO8859-1/articles/setup-serialem-for-k2/article.xml 1 2013-07-15 11:49:00 xuchen Exp$

Some people have asked how to setup SerialEM to work with Gatan's direct detector K2 camera. Based on our own experience with Tecnai F30, I piled up the steps here to help you for some initial configurations.

Before K2 time, SerialEM is always installed on the same computer on which Gatan DigitalMicrogaph runs. It can be either just the same computer of Tecnai with DigitalMicrogaph installed or a separate computer that only DigitalMicrogaph runs on. In later case, a simulation version of Tecnai should be also installed so that SerialEM controls microscope through the Tecnai simulation layer.

However, this configuration no longer works for K2 camera. K2 computer is on 64-bit Windows 7 operation system. There is no version of Tecnai is available for this OS yet. SerialEM has to be installed on Tecnai computer and controls DigitalMicrogaph remotely. To do that, SerialEM has made some changes including using socket network to communicate with DigitalMicrogaph on K2 computer.

This document is mainly made for these changes. It is based on the instruction received from David Mastronarde when we first setup our K2 system on our Tecnai F30. It should work for Titan scope too. A pdf version of this document is also available.


Table of Contents
1 Setup Steps
2 A Note on K2 Computer Memory Size

1 Setup Steps

  1. Make sure both Tecnai and K2 computers are on the same local area network (LAN). In our case, Tecnai F30 computer has IP address 192.168.1.2, while K2 computer has IP address 192.168.1.5.

  2. Put SEMCCD-GMS2-64.dll in the "C:\ProgramData\Gatan\Plugins" folder on the K2 Win 7 computer. Since 3-3-0 release, this file is part of the package. After unzipping the installation exe file SerielEM_3-3-0.exe, you will find this file in the unzipped folder.

  3. Pick a TCP port to use. David suggests 48890.

  4. Define an environment variable on the Win 7 box SERIALEMCCD_PORT with a value of that number, 48890 in this case. Here is how to do it.

    • Right click on "my computer" from desktop icon or from "Start" button → "properties". This will bring up the System window.

    • Click on "Advanced System Settings". This will bring up "System Properties" window, as below.

    • Click on "Environment Variables" button near the bottom. This brings up "Environment Variable" window, as below.

    • Click on "New" button, and input variable name and value in the boxes, as shown below. On our current K2 computer, there is only one account. Therefore, it is fine to define User variable. For multiple users login system, the System variable should be defined instead.

    • It would be useful to also define variable for debug, as shown below.

  5. Open this port on firewall softwares on both Tecnai and K2 computers. Worst case, turn firewall off.

  6. On Tecnai computer, install the latest SerialEM version. At the time of writing this document, it is version 3.3.0.

  7. In property file, add following to general property section.

    
RemoteDMReferencePath   C:\ProgramData\Gatan\Reference Images
    # added for remote DM access
    GatanServerIP   192.168.1.5
    GatanServerPort 48890
    K2FilterName    Hanning Window (default)
    K2FilterName    Bandpass Filter (default)
    K2FilterName    Sobel Filter (default)
    K2FilterName    Combined Filter (default)
    

    And put following lines into individual camera property section. Here it is complete section for our K2.

    
CameraProperties        1
    Name    K2 Summit
    DMGainReferenceName     K2-0001 1 Gain Ref. x1.m0.dm4
    CameraSizeY     3840
    CameraSizeX     3712
    SizeCheckSwapped   1
    RotationAndFlip   7
    #UsableArea 0 0 7680 7424       # top left bottom right!
    UsableArea 0 0 3712 3840        # top left bottom right!
    UseSocket       1
    #AdvancedType    1
    K2Type  1
    MakesUnsignedImages     1
    XMustBeMultipleOf       4
    YMustBeMultipleOf       2
    FourPortReadout 0
    Binnings        1 2 3 4 5 6 8
    BasicCorrections        49
    HotPixelsAreImodCoords  1
    #DarkXRayAbsoluteCriterion      20
    #DarkXRaySDCriterion    15
    #DarkXRayRequireBothCriteria    1
    MaximumXRayDiameter     6
    BeamBlankShutter        0
    OnlyOneShutter  1
    #SetAlternateShutterNormallyClosed 1
    StartupDelay  2.435
    ExtraBeamTime  0.3
    BuiltInSettling  0.0
    ShutterDeadTime 0.001
    MinimumDriftSettling    0.05
    ExtraBeamTime   0.05
    MinimumBlankedExposure 0.35
    ExtraUnblankTime        0.012
    ExtraOpenShutterTime    0.12
    Retractable     1
    InsertionDelay  5.0
    RetractionDelay 3.0
    GIF     0
    Order 1
    FilmToCameraMagnification       1.31    # orig=1.342
    PixelSizeInMicrons      5.0
    CountsPerElectron       38.44
    ExtraRotation   0.
    # MagIndex  DeltaRotation (999 not measured)  SolvedRotation (999 not
    # measured)   Pixel size (nm, 0 not measured)
    ##RotationAndPixel 33 0.04 999 0.0749
    RotationAndPixel 4 999 999 26.667
    RotationAndPixel 5 999 999 18.300
    RotationAndPixel 6 999 999 13.381
    RotationAndPixel 7 999 999 10.590
    RotationAndPixel 8 999 999 9.194
    RotationAndPixel 9 999 999 6.657
    RotationAndPixel 10 999 999 5.574
    RotationAndPixel 11 999 999 4.116
    RotationAndPixel 12 999 999 3.378
    RotationAndPixel 13 999 999 2.870
    RotationAndPixel 14 999 999 2.222
    RotationAndPixel 15 999 999 1.961
    RotationAndPixel 16 999 999 1.69
    ## M and SA below, starting 2300 (screen up)
    RotationAndPixel 17 159.82 999 1.651
    RotationAndPixel 18 0.12 999 1.24
    RotationAndPixel 19 0.15 999 0.9811
    RotationAndPixel 20 0.08 999 0.8253
    RotationAndPixel 21 -0.27 999 0.4224
    RotationAndPixel 22 0.07 999 0.3344
    RotationAndPixel 23 0.38 80.3 0.2543
    RotationAndPixel 24 -0.03 999 0.197
    RotationAndPixel 25 0.05 80.2 0.1685
    RotationAndPixel 26 0.09 999 0.1226
    RotationAndPixel 27 0.04 999 0.1007
    RotationAndPixel 28 90.33 170.7 0.0659
    RotationAndPixel 29 0.05 999 0.0502
    RotationAndPixel 30 999 999 0.04225
    RotationAndPixel 31 999 999 0.0341
    RotationAndPixel 32 999 999 0.0256
    RotationAndPixel 33 999 999 0.02025
    #RotationAndPixel 34 999 999 0.0516
    #RotationAndPixel 35 999 999 0.0387
    #RotationAndPixel 36 999 999 0.0309
    #RotationAndPixel 37 999 999 0.0255
    #RotationAndPixel 38 999 999 0.0190
    #RotationAndPixel 39 999 999 0.0149
    EndCameraProperties