Installation

Prerequisites for the FEI or Thermo Fisher Scientific microscope:

  • TEM Scripting

  • TEM Advanced scripting (optional)

  • LowDose (optional)

  • TecnaiCCD plugin for Digital Micrograph (optional)

  • SerialEMCCD plugin for Digital Micrograph (optional)

Requirements for this package:

  • python 3.4 or newer

  • comtypes

  • mrcfile (to save MRC files)

  • numpy

  • pillow (to save non-MRC files)

  • imageio (optional, to speed up image acquisition)

Online installation on Windows

This assumes you have connection to the Internet. Execute from the command line (assuming you have your Python interpreter in the path):

py -m pip install --upgrade pip
py -m pip install pytemscript

Offline installation on Windows 7 or 10

The command below will download pytemscript and its dependencies on a computer connected to the Internet. We assume your microscope PC runs Windows 7 or Windows 10 64-bit OS. You need to know the Python version on the microscope PC (example below is for 3.8):

pip download -d . pytemscript --python-version 38 --only-binary=:all: --platform win_amd64

Copy downloaded *.whl files to the target PC and install them:

py -m pip install pytemscript --no-index --find-links .

If you want to install pytemscript from sources instead, download them from GitHub. You will still need the wheel files for dependencies:

py -m pip install numpy comtypes mrcfile pillow --no-index --find-links .
py -m pip install -e <source_directory>

Installation on Linux

This assumes you want to setup a remote client and have already installed pytemscript on the microscope PC (Windows) which will run a server. The installation commands are the same as above:

pip install pytemscript

Installation on Windows XP 32-bit

Latest supported Python version on Windows XP is 3.4. Download pytemscript and its dependencies on a computer connected to the Internet:

pip download -d . pytemscript comtypes==1.2.1 mrcfile==1.3.0 numpy==1.15.4 pillow==5.3.0 typing --python-version 34 --only-binary=:all: --platform win32

Copy downloaded *.whl files to the target PC and install them:

py -m pip install pytemscript typing --no-index --find-links .

Testing

The package provides a few command-line scripts to test the microscope interface connection and image acquisition:

pytemscript-test
pytemscript-test-acquisition
pytemscript-test-events