FEI Talos installation specifics¶

Install win32 version of python subpackages¶

Because all interaction with the scope uses COM interface that is only accessible through 32-bit architecture, python running Leginon component is the 32-bit version. 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.

Talos On-system UI uses 32-bit python as well. Therefore we just need to install the dependency that is missing in there. The location of this python is

C:\Tecnai\OnSystemUI\Python27

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

• If the system comes pre-installed with 64-bit python as well, some of these packages may get confused.*
  During these installation, Keep an eyer on where the packages are installed into. If it attempts to install into the 64-bit python at C:\Python27, contact Leginon Team through Forum.

The rest of the installation is similar to other FEI systems.

(Strongly recommended) Use local myami folder to run Leginon¶

Because we install into FEI's framework folder, it may be erased at the next upgrade by the service engineer. To reduce the possibility of loss of local modification, we recommend using local myami checked out from NRAMM svn repository directly, rather than installed into python's site packages.

Set pythonpath environment variable for local myami sandbox¶

For an uninstall myami svn checkout, you can set PYTHONPATH environment variable to use it directly.

1. Control Panel\All Control Panel Items\System> click on Advanced settings
2. System Properties\Advanced> click on Environment Variables
3. Either create a new variable for the current user, or do it system-widely.

PYTHONPATH should incldue both the base myamipath as well as leginon

For example, myami folder is at C:\Users\vagrant\Desktop\myami, then the python path should be set as follows:

C:\Users\vagrant\Desktop\myami; C:\Users\vagrant\Desktop\myami\leginon

instruments.cfg¶

cs is constant for sperical abberation

For Tecnai series:

[TEM]
class: tecnai.Talos
cs: 2.7e-3

Testing with pyscope¶

In python command

from pyscope import tecnai
t = tecnai.Talos()
t.getMagnification()

Trouble Shooting¶

unable to initializ Tecnai interface error

Programs to open before Leginon Client: None¶