Leginon

h1. Test Leginon on the Computer Controlling the Microscope

h2. Using a Gatan Camera

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

*  insert the Gatan CCD in Digital Micrograph.

h2. Using a Tietz Camera

*  Close Tietz TCL program

*  Put camera switch box to select CCD.

h2. 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.

<pre>[Tem]

tecnai.Tecnai

[Cam1]

gatan.Gatan

[Cam2]

tietz.TiezFastScan</pre>

h2. 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".

!http://emg.nysbc.org/software/leginon/images/icons/calculate.png!

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.

h2. 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.

h2. Check on the Web viewer

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

Chapter</link>.

h2. 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.

h2. 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.

______

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

______