Leginon

h1. Additional installation on the microscope computer

The full leginon and its supporting packages need to be installed on the Windows computer

controlling the microscope. Additional programs are required for communication with the CCD

and extra functions for Tecnai scripting not supported as default by FEI Tecnai

microscopes

h2.  Required supporting programs for the CCD camera from camera makers

Install and register the following programs for CCD cameras from the two makes:

|_.Camera Make:|_.File:|

| Gatan|TecnaiCCD.dll|

| Tietz|CAMC4.exe*|

*Note:* We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. Replacing it with an earlier version of CAMC4.exe resolved the problem.

h2. Additional Package required from NRAMM for Gatan camera or camera that uses TIA

For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install

with python

|_.SVN Package Name|_.Installed Python Package Name|_.Reason for update:|

|comarray|comarray|com module output conversion to array|

* [[Windows installation#Check-out-SVN-Source-Files-from-the-depository|Check out the comarray package]] from svn depository with your SVN client

<pre>cd Leginon-1.6-ALL

svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray</pre>

* Start a command line Window from Start Menu

* Install the package with commands such as

<pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray

c:\\python25\python.exe setup.py install</pre>

h2.  Supporting programs for film exposure

Install the following if you need film exposure on FEI Tecnai TEM through Leginon,

available through FEI. Please contact Max Otten: mto@feico.com and request

for adaexp.exe that works with your version of Tecnai user interface program.

|_.Name:|_.File:|

| exposure adaptor|adaexp.exe|

h2.  Register adaexep.exe

*  From the command prompt:

<pre>adaexp.exe /regserver</pre>

*  From the program start menu under pyScope or C:\Python25\Lib\site-packages\pyScope\

<pre>updatecom.py</pre>

h2. Modify instruments.cfg:

Sinedon now has full control of database interaction, therefore, the database

configuration in leginon.cfg is no longer needed.

* Modify the file instruments.cfg in the installed pyScope directory to that for

your microscope and camera. For example, if your microscope uses Tecnai Scripting

Interface and you have a Gatan camera that you interface through DigitalMicrograph:

<pre>[tem]

class: tecnai.Tecnai

[camera]

class: gatan.Gatan</pre>

The file contains other examples of microscope and camera drivers that we

distribute from NRAMM.

h2. Run updatecom.py

From a command line window:

<pre>cd C:\python25\Lib\Site-Packages\pyScope

C:\python25\python.exe updatecom.py</pre>

This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py,

in the same directory.

h2. Additional setup on Tietz PXL camera (optional)

The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like

to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that

get camera dimension in tietz.py of pyScope package.

*  Go to C:\Python25\Lib\site-packages\pyScope\

*  Edit tietz.py with a plain text editor

*  Find the lines:

<pre> def getCameraSize(self):

# {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}}

x = self._getParameterValue('cpTotalDimensionX')

y = self._getParameterValue('cpTotalDimensionY')

return {'x': x, 'y': y}

</pre>

*  Change the last line to:

<pre>    return {'x': 2048, 'y': 2048}</pre>

h2.  Additional Software (Optional):

TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room

just to open the column valves.

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[[Windows Installation|< Windows Installation]] | [[Next Steps|Next Steps >]]

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