Skip to content

Installation Guide

Dependencies

  • Python 3.9+
  • FIB/SEM microscope (a commercial product by ThermoFisher FEI or TESACN)
  • Autoscript software (a commercial product by ThermoFisher FEI)
  • tescanautomation software (a commercial product by TESCAN)

Python

Python 3.9+ is required. The Anaconda distribution of python is recommended.

Setting up your python virtual environment

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.)

Create a new virtual environment from the Anaconda Prompt terminal:

$ conda create -n fibsem python=3.9 pip
$ conda activate fibsem
$ pip install autolamella

Installing from source

Clone this repository, and checkout v0.2-stable: 

$ git clone https://github.com/DeMarcoLab/autolamella.git
$ git checkout origin/v0.2-stable

Create an environment and install the package:

$ conda create -n fibsem python=3.9 pip
$ conda activate fibsem
$ pip install -e .

Running Autolamella

Open the Anaconda Prompt terminal and run the following commands.

$ conda activate fibsem
$ autolamella_ui

Installing the commercial microscope APIs

For instructions and trouble shooting tips for installing the microscope APIs, see Installation Guide.