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 installation 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|

* comarray is part of the checkout package you downloaded from our repository

<pre>cd Leginon2.0/comarray

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\Leginon2.0\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:

* 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>

The python window appears should say show the required type libraries it found:

<pre>

Generating .py files from type libraries...

initializing TEM Scripting Error, cannot find typelib for "TEM Scripting"

initializing Tecnai Scripting done.

initializing TOM Moniker done.

initializing Tecnai Low Dose Kit done.

initializing Tecnai Exposure Adaptor done.

initializing Tietz CCD Camera done.

</pre>

The output is of course depending on what is available on your microscope computer.  You should have either "Tecnai Scripting" or the pairing of  "TEM Scripting" and "TOM Moniker".

The script should generate a few files in C:\\python25\Lib\win32com\gen_py with seemly scrambled names such as BC0A2B03-19FF-11D3-AE00-00A024CBA50Cx0x1x9.py

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.

______

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

______