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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

Install the software pre-requisites

Python

Python 3.6 is required. The Anaconda distribution is recommended.

It is also highly recommended to use virtual environments for development, see Managing Conda Environments for more information. (Optionally, you could use virtualenv if you prefer.)

Run these commands in your terminal to create a new virtual environment called piescope:

conda create -n piescope python=3.6 pip
conda activate piescope

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

Add the autoscript python packages to your site-packages

You may find that the default AutoScript installation came bundled with a copy of Python 3.5, instead of the newer Python 3.6 this project requires.

If that is the case, you can copy the relevant python autoscript packages into the site-packages of your own python 3.6 environment. See Managing Conda Environments for more information.

To add the AutoScript python packages to your new conda environment, follow these three steps:

  1. Find the python environment that was created with your AutoScript installation. Typically, you can expect the environment is named 'Autoscript', and its installed packages should be found at: C:\Program Files\Python35\envs\AutoScript\Lib\site-packages\

Troubleshooting: If you're having trouble finding the location AutoScript chose to install its python packages into, you can open the default terminal on your machine (eg: cmd for Windows) and type where python (Windows) or which python (Unix). The result will be something like C:\Program Files\Python35\envs\AutoScript\python.exe. *Navigate to the environment location (in the example here, that's C:\Program Files\Python35\envs\AutoScript\ * then change directories into Lib, and then the site-packages directory. This is where the python packages live.

  1. Find the conda environment location you just made called autolamella-dev. ...conda/envs/autolamella-dev/Lib/site-packages/

Troubleshooting: If you're having trouble finding the conda environment location for autolamella-dev you can open the Anaconda terminal on your machine and type where python (Windows) or which python (Unix). The result will be something like C:\Users\yourusername\.conda\envs\autolamella-dev\python.exe *Navigate to the environment location (in the example here, that's C:\Users\yourusername\.conda\envs\autolamella-dev\ * then change directories into Lib, and then the site-packages directory. This is where you want to add copies of the AutoScript python packages.

  1. Make a copy of the relevant AutoScript python packages into the conda environment. You will need to copy:
  • autoscript_core
  • autoscript_core-5.4.1.dist-info
  • autoscript_sdb_microscope_client
  • autoscript_sdb_microscope_client_tests
  • autoscript_sdb_microscope_client_tests-4.2.2.dist-info
  • autoscript_sdb_microscope_client-4.2.2.dist-info
  • autoscript_toolkit
  • autoscript_toolkit-4.2.2.dist-info
  • thermoscientific_logging
  • thermoscientific_logging-5.4.1.dist-info

Check the AutoScript python packages work in your environment

You can check that this has worked by opening the Anaconda terminal, then typing:

conda activate autolamella-dev
python

And then at the python prompt:

from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()

If there is no ImportError raised, then you have been sucessful.

Install the Pylon Software Suite and pypylon python library

Install the 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/

Install the 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 piescope

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

Python package dependencies

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

  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

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.