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Software Installation Guide

Dependencies

Hardware requirements

  • FIB/SEM microscope (a commercial product by ThermoFisher FEI)
  • Basler detector (https://www.baslerweb.com)
  • Toptica lasers (for the fluorescence microscope)
  • SMARACT stage (controlling the fluorescence objective lens position)

Software requirements

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 4.2.2

The version numbers of the python packages autoscript installs were:

  • autoscript-core 5.1.0
  • autoscript-sdb-microscope-client 4.2.2
  • autoscript-sdb-microscope-client-tests 4.2.2
  • autoscript-toolkit 4.2.2
  • thermoscientific-logging 5.1.0

Installing the Pylon Software Suite and pypylon python library

Pylon software suite

The Pylon software suite is produced by Basler for use with their detectors. Instructions for downloading and installing the latest version of Pylon can be found on their website: https://www.baslerweb.com/en/products/software/basler-pylon-camera-software-suite/

pypylon python package

Basler also provide a Python API for use with their detectors and the Pylon software suite. Instructions for downloading and installing the latest version can be found at: https://github.com/basler/pypylon

Install the piescope back-end library

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

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

pip install $PIESCOPE_WHEEL_FILENAME.whl

Install piescope_gui

Download the latest release of the piescope_gui source code from https://github.com/DeMarcoLab/piescope_gui/releases

Unzip and then pip install piescope_gui:

cd piescope_gui
conda activate piescope_gui
pip install .

Python package dependencies

All the python package dependencies you need should be installed automatically, with the exceptions:

  1. Autoscript which is a commercial product and requires a special license key.
  2. The Basler pypylon python pacakge, made freely available at https://github.com/basler/pypylon
  3. The piescope back-end library, made freely availble at https://github.com/DeMarcoLab/piescope/releases

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.