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INSTALLATION.md

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Installation Guide

Dependencies

  • Python 3.6
  • FIB/SEM microscope (a commercial product by ThermoFisher FEI)
  • Autoscript software (a commercial product by ThermoFisher FEI)

Python

Python 3.6 is required.

Installing Autoscript

Autoscript provides an API (application programming interface) for scripting control of compatible FEI microscope systems. This is a commercial product by Thermo Fisher FEI, please visit their website at https://fei.com for information on pricing and installation.

We use Autoscript version 4.1.0

The version numbers of the python packages autoscript installs were:

  • autoscript-core 5.1.0
  • autoscript-sdb-microscope-client 4.1.0
  • autoscript-sdb-microscope-client-tests 4.1.0
  • autoscript-toolkit 4.1.0
  • thermoscientific-logging 5.1.0

Install autolamella

Download the latest autolamella release wheel from https://github.com/DeMarcoLab/autolamella/releases

Pip install the wheel file (.whl) into your python environment.

pip install $AUTOLAMELLA_WHEEL_FILENAME.whl

Python package dependencies

All the python package dependencies you need should be installed automatically, with the exception of Autoscript which requires a special license key.

If you do encounter an issue with missing package dependencies, you can always try reinstalling them with:

pip install -r requirements.txt

Having problems?

  • Check to see if Autoscript is correctly installed and configured.
  • Check to see if your python environment contains all packages listed in the requirements.txt
  • Check that when you call python from the terminal, you get the python environment containing the dependencies listed above (i.e. you are not using a different python environment)
  • Try cloning the repository and running the unit tests, you may want to try installing from the source code.