Tietz camera installation and setup¶

Many Tietz cameras are 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.

Extra Package and Installation¶

program/package	notes
CAMC4.exe	(Should come with the camera)

Register CAMC4.exe

• From the command prompt, run the following commands.
  

  CAMC4.exe /regserver

Run updatecom.py sould contain this output

initializing Tietz CCD Camera done.

Register the Tietz ping callback function. From a command line window:¶

cd C:\python27\Lib\Site-Packages\pyscope
C:\python27\python.exe tietzping.py

instruments.cfg¶

The camera modes are configured as separate cameras as follows.

• Super Resolution should be double the size of Linear and Counting.
• zplane will be relative to any other cameras in your system. Anything below K2 should have a lower zplane.
• to make the images acquired from the camera to have the standard Leginon orientation, the camera configuration in Digital Micrograph will need a rotation and flip (270 degree rotation and a flip around the vertical axis on our camera) on typical FEI F20 but maybe not so post-GIF or on Krios. Therefore, the height is longer than width in the configuration below

[Gatan K2 Linear]
class: dmsem.GatanK2Linear
zplane: 50
width: 3710
height: 3838

[Gatan K2 Counting]
class: dmsem.GatanK2Counting
zplane: 50
width: 3710
height: 3838

[Gatan K2 Super]
class: dmsem.GatanK2Super
zplane: 50
width: 7420
height: 7676

If you have an Orius camera with K2, set its zplane below K2 like this:

[camera2]
class: dmsem.GatanOrius
zplane: 49
width: 2048
height: 2048

Setup¶

• Set camera configuration to 270 degree rotation and horizontal flip to give the standard Leginon orientation.
• Create the folder to store the dose fractionation raw frames. Default location is D:\\frames.
• Setup raw frame file transfer from a network data server.

Testing with pyscope¶

1. Start DigitalMicrograph
2. From python command line or IDLE:

   import pyscope.dmsem
   k = pyscope.dmsem.GatanK2Counting()
   k.setExposureTime(200)
   k.getImage()

You should expect these to run without error. The getImage() command should give a 2D numpy array like

array([[1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         ...,
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],dtype=int16)

The number and dtype depends on the camera.

a.shape command should give a tuple of the camera dimension matching your camera.
For example, (4096,4096)

If you use python shell to do this test, some of the error will cause the shell window to close immediately. Use Python IDLE instead in that case

Testing frame saving¶

You can continue the test above by saving frames, too.

k.setSaveRawFrames(True)
k.setExposureTime(200)
a=k.getImage()
a.shape

* The last command should give you the shape of the summed image, and the frame movie should show up on your frames directory

testing energy filter¶

1. Start DigitalMicrograph
2. From python command line or IDLE:

   import pyscope.dmsem
   k = pyscope.dmsem.GatanK2Counting()
   k.getEnergyFiltered()
   k.getEnergyFilter()
   k.setEnergyFilter(True)
   k.getEnergyFilter()
   k.setEnergyFilter(False)
   k.getEnergyFilter()
   k.getEnergyFilterWidth()
   

Trouble shooting¶

When Leginon initializes the camera, a program called CAMC4 should start automatically in the backgound. This is confirmed by the little camera icon showing up in the system tray in the lower right of the screen. Also, task manager can be started to confirm CAMC4 is running. Sometimes problems occur if more than one CAMC4 is running at the same time, so task manager will help identify this.

If Leginon is not initializing the camera or not getting proper images, you should first test image acquisition using TVIPS software to make sure it is not a hardware issue. Use TCL or there is a test program called TestMFCCamera that can acquire an image and test the CAMC4 operation.

Programs to open before Leginon Client: Digital Micrograph¶