Windows Package Requirement¶

General

Python and Support Packages (Note that python 2.7 must be used to match window installers of myami modules):¶

You should generally be able to use the most recent versions of these packages that are available from their respective web sites. Just be sure to always get the version that is compatible with Python 2.7. However, you must use the exact version for numpy. If you are having trouble with the most recent version, try to use the specific versions we include in http://emg.nysbc.org/projects/leginon/files

Program	package web site	local copy of win32 installer	local copy of amd64 installer
Python > 2.7.10	http://www.python.org	python-2.7.16.msi	python-2.7.18.amd64.msi
wxPython 2.8 or newer	http://www.wxpython.org	wxPython2.8-win32-unicode-2.8.12.1-py27.exe	wxPython2.8-win64-unicode-2.8.12.1-py27.exe
MySQL Python client 1.2 or newer	http://sourceforge.net/projects/mysql-python	MySQL-python-1.2.4b4.win32-py2.7.exe	MySQL-python-1.2.3.win-amd64-py2.7.exe
Python Imaging Library (PIL) 1.1.4 or newer	http://www.pythonware.com/products/pil/	PIL-1.1.7.win32-py2.7.exe	PIL-fork-1.1.7.win-amd64-py2.7.exe
NumPy	(use only from our file to match compiled numextension	numpy-1.7.0-win32-python2.7.exe	numpy-MKL-1.6.2.win-amd64-py2.7.exe
SciPy 0.5.1 or newer	http://www.scipy.org	scipy-0.11.0-win32-superpack-python2.7.exe	scipy-0.11.0.win-amd64-py2.7.exe

Use pyMySQL for leginon 3.6 and above instead of MySQL Python client for both win32 and 64.

pyMySQL 0.10.1 (not higher)

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

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

(trunk, beta, 3.3 and up) GIT client used for check out from our repository¶

We have switched to git revision control recently. If you want to install the newest changes, you need to use the files from git repository.

You can clone our repository with

Name:	Download site:
git for Windows	https://git-for-windows.github.io

• During the installation, select "Checkout as-is, commit as-is" option at the step regarding automated translation of CRLF and LF line endings if you are a developer and may commit changes.
• Default is fine with the rest of the options.

Packages from NRAMM¶

Most of the subpackages from NRAMM are obtained through our repository. You have two option depending on your situation

1. Clone from git repository (newer version)
2. Copy your git clone or svn checkout from your linux box if you do not have internet access on instrument PC.

Cloning myami git repository¶

We recommend using git bash to do so which gives most freedom in configuration and so that you can use unix syntax.
git for windows cloning

• Right Click at the folder where it will contain your clone and choose "Git Bash Here" to start the shell window.

• With Windows XP "Git Bash Here" does not appear with right-click. In this case, you can start git bash from Start menu/Programs/Git/Git Bash and move the folder created to where you want it to be.

To checkout (called clone in git) the package from NRAMM:¶

See Acquiring NRAMM Repository files for different examples and match the repository with what you do on the Linux side.

numextension windows installer¶

Because numextension and would require extra compilers if you build them yourself, we have created Windows installers for them for python 2.7 and made them available at /redmine/projects/leginon/files.

These are the current Leginon python 2.7 compiled packages you should install by opening them on Windows.¶

Package	win32	amd64
numextension	numextension-svn.win32-py2.7-numpy1.7.0.exe	numextension-svn.win-amd64-py2.7-numpy1.6.2.exe

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Windows Installation That apply to all instruments >

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Additional Requirement on the microscope

FEI Tecnai/Titan¶

TEM Scripting or Tecnai Scripting	Request this when purchasing the microscope	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
Advanced TEM Scripting	Request this when purchasing the microscope	Required if you have Selectris or Falcon Camera

JEOL¶

Depending on setup. See JEOL External3 setup

Additional Requirement for cameras

Gatan camera controlled by Digital Micrograph installed on FEI Tecnai/Titan microscope computer.¶

program/package	notes
TecnaiCCD.dll

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

Gatan K2/K3 camera and its associated Orius camera controlled by Digital Micrograph installed on stand-alone 64-bit computer.¶

SerialEM DigitalMicrograph Plug-in. Get only what you need for your Digital Micrograph version.

DM version	local copy of SerialEM SEMCCD	description
2.2.x	SEMCCD-GMS2-64.dll	DM for 64-bit GMS 2.0 - 2.2
2.3.0	SEMCCD-GMS2.30-64.dll	DM for 64-bit GMS 2.30
2.3.1, 2.3.2, 3.0	SEMCCD-GMS2.31-64.dll	DM for 64-bit GMS 2.31 and above
3.31 and above	SEMCCD-GMS3.31-64.dll	DM for 64-bit GMS 3.31 and above

Note: DM = Digital Micrograph; GMS = Gatan Microscopy Suite
32bit versions also exit, but not for GMS 2.31 and above

TIA-controlled camera (FEI Eagle, FEI Falcon, and Gatan Orius used with Falcon¶

program/package	notes
Tia.dll	(Should come with the microscope)

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

Tietz camera¶

program/package	local win32 installer
Python for Windows extension (pywin32)	pywin32-218.win32-py2.7.exe

program/package	notes
CAMC4.exe	(Should come with the camera)

Direct Electron camera¶

program/package	notes
DirectElectronAPI.exe	(Should come with the camera)
Google protobuf	portobuf installation instruction

Film (Only for FEI Tecnai/Titan)¶

program/package	notes
adaexp.exe	This is the exposure adaptor. Contact Max Otten: mto@feico.com and request for adaexp.exe that works with your version of Tecnai user interface program.

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Installation >

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