Test Leginon on the Computer Controlling the Microscope¶

Using a Gatan Camera¶

• Open Digital Micrograph (or check that the Tietz software is closed).

• insert the Gatan CCD in Digital Micrograph.

Using a Tietz Camera¶

• Close Tietz TCL program

• Put camera switch box to select CCD.

Set up instruments.cfg in the installed pyScope folder¶

• goto C:\Python25\Lib\Site-Packages\pyScope

• open instruments.cfg with a text editor and add the following according to your
  tem and camera. Enter only what you have!

For example, if your scope uses tecnai scripting and has both a Gatan camera
interfaced by Digital Micrograph and a side-entry-above the specimen Tietz Fast Scan
camera, you should enter the following.

[Tem]
tecnai.Tecnai

[Cam1]
gatan.Gatan

[Cam2]
tietz.TiezFastScan

Start Leginon on the Microscope computer & Import Magnifications¶

• scope> Start Leginon (Either with the shortcut on the Desktop or follow the
  Start Menu-\Start\Programs\Leginon>Leginon)

• Leginon Setup Wizard> select "Create session" in session type. Even though you
  have created a session for simulation test, if the other machine uses linux os, it is
  better to create a new session so that the path mapping difference betwee Windows and
  Linux does not cause confusion.

• Fill in session name and comments. Comments will appear in Viewers

• Select instrument and project, if project database is used. Image path is
  automatically selected.

• Image path is automatically selected based on your leginon.cfg file.

• Choose "Finish" in the set up wizard to start the session.

• Leginon/Main menu/Application> select "Run...." and choose the application
  named "Manual", both "main" and "scope" launchers will be set to the scope computer,
  and then launch the application.

• Leginon/Node Selector> select Instrument node.

• Leginon/Instrument> check that TEM is selected to display the
  parameters.

• Left-click on the tool "Get Magnification".

This will import the valid TEM magnification from the microscope into the
database.

• During Leginon run an Application Error Message may pop up saying

<blockquote>

"Exception EAccessViolation in module adaExp.exe at ....

Access violation at address xxxx in module 'adaExp.exe'. Read of address
xxxx"

</blockquote>

Do NOT touch this message box, or leginon client will need restarting.

Acquiring the first real image¶

• scope> make sure you have beam and something other than a blank to image on
  the CCD.

• Leginon/Application/Run> select Manual Application.

• Leginon> From the list of nodes on the left panel, select Manual node.

• Leginon/Manual> Open the "Setting" tool and configure the settings:

Your TEM and CCDCamera should be available for selection.

Acquisition/Camera Configuration- use one of the preconfigured selection for
binning and size such 512x8.

Save image to the database=yes.

Leave the rest of the configuration to default.

• You should see your first real image acquired through Leginon in the image
  display panel.

Check on the Web viewer¶

Follow the <link linkend="AppManual_webviewer">instruction in Manual Application
Chapter</link>.

Closing Leginon program on Windows¶

The best way to close Leginon program is to close the python command window (normally
black) that shows up when the Leginon GUI appears since Leginon GUI window on Windows is
controlled through the python command window

If you first close the GUI window, the python process is not ended. Therefore, the
latter become frozen and you will have to wait for TaskManager to ask you to close the
broken process.

Problem solving for the first mircoscope test¶

Most common problem at this point is that your TEM or CCDCamera does not show up in
Leginon for use. It is caused by lack of proper functioning or non-communicating microscope
scripting or CCD drivers to Leginon system's python wrapper in pyScope package. See <link
linkend="InstT_testrun">Installation Troubleshooting</link> and "pyScope Bulletin Board regarding
"testing if pyScope is working"":http://emg.nysbc.org/bb/viewforum.php?t=246 for more.

If everything goes smoothly, test the network connection as in the next section and then
do the same above image acquisition test through from the remote computer.

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< Test Leginon with Simulator | Test Network Connection Between Remote and Microscope Computers >

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