FEI Tecnai Titan installation specifics¶

Install win32 version of python subpackages¶

Use the 32-bit Windows files (those marked as win32 and certainly not the ones says 64) in http://emg.nysbc.org/projects/leginon/files for these.

Here is the full list

Program	package web site	local copy of win32 installer
Python 2.7.16	https://www.python.org	python-2.7.16.msi
wxPython 2.5.2.8 or newer	https://www.wxpython.org	wxPython2.8-win32-unicode-2.8.12.1-py27.exe
Python Imaging Library (PIL) 1.1.4 or newer	http://www.pythonware.com/products/pil/	PIL-1.1.7.win32-py2.7.exe
NumPy	(use only from our file to match compiled numextension	numpy-1.7.0-win32-python2.7.exe
SciPy 0.5.1 or newer	http://www.scipy.org	scipy-0.11.0-win32-superpack-python2.7.exe

Leginon 3.5 or before

MySQL Python client 1.2 or newer

http://sourceforge.net/projects/mysql-python

MySQL-python-1.2.4b4.win32-py2.7.exe

Leginon 3.6 and up

pyMySQL 0.10.1 (not higher)

https://pypi.org/project/PyMySQL/

pyMySQL-0.10.1-py2.py3-none-any.whl

Program	package web site	local copy of win32 installer
comtypes 0.6.2	http://sourceforge.net/projects/comtypes"	comtypes-0.6.2.win32.exe

Required scripting from FEI¶

TEM Scripting or Tecnai Scripting	Request this when purchasing the microscope	Required
TomMoniker Scripting	Should come with TEM Scripting	Required
Low Dose Server Library	Should come with the microscope if low dose kit was purchased	Required only if you want to use low dose kit with Leginon's Manual Application

Run checkcom.py¶

• From a command line window:
  

  cd C:\python27\Lib\site-packages\pyscope
  C:\python27\python.exe checkcom.py

• The output should at least find typelib for
  

  TEM Scripting
  

  
  and
  

  TOM Moniker
  

If you have Low Dose Kit

Tecnai Low Dose Kit

You will only find Tecnai Exposure Adaptor (Scripting for film exposure) if you ask FEI for it.

instruments.cfg¶

cs is constant for sperical abberation

For Tecnai series:

[TEM]
class: fei.Tecnai
cs: 2.0e-3

For Halo (Titan column with tecnai compustage):

[TEM]
class: fei.Halo
cs: 2.7e-3

For Krios (different compustage)

[TEM]
class: fei.Krios
cs: 2.7e-3

For Krios EF mode, treated as a separate instrument. i.e. add

[TEM]
class: fei.EFKrios
cs: 2.7e-3

Setup fei.cfg¶

fei.cfg replaces various constants set inside the old tecnai.py that some local installation tend to change. The separate cfg file allows easier update to future releases.

• A template for fei.cfg is in the installed pyscope directory as "fei.cfg.template". Copy it to
  

  C:\Programs File (x86)\myami\fei.cfg

The template file is configured with the default behavior. No change is required normally.

If you are upgrading and have changed tecnai.py, please make the corresponding changes in fei.cfg. If you do not find the option, please let Leginon development team know.

Testing with pyscope¶

For Tecnai series In python command

from pyscope import fei
t = fei.Tecnai()
t.getMagnification()

For Krios

from pyscope import fei
t = fei.Krios()
t.getMagnification()

For Krios with EF-TEM mode, activate EF-TEM mode on the scope, and then do the following

from pyscope import fei
t = fei.EFKrios()
t.getMagnification()

For Halo

from pyscope import fei
t = fei.Halo()
t.getMagnification()

You should get the current magnification at the microscope when the main viewing screen is up

Trouble Shooting¶

unable to initializ Tecnai interface error

Programs to open before Leginon Client: None¶