autolamella

autolamella

Automatated ion beam milling for cryo-electron microscopy sample preparation.

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AutoLamella is a python package for automated cryo-lamella preparation with focused ion beam milling. It is based on openFIBSEM, and currently supports the TESCAN Automation SDK and ThermoFisher AutoScript. Support for other FIBSEM systems is planned.

Documentation

Documentation Site

Install

Create a new virtual environment from the Anaconda Prompt terminal:

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

Running Autolammela

Open the Anaconda Prompt terminal and run the following commands.

conda activate fibsem
autolamella_ui

ui_new

To launch liftout related methods:

conda activate fibsem
autoliftout_ui

Citation

If you find this useful, please cite our work.

Genevieve Buckley, Gediminas Gervinskas, Cyntia Taveneau, Hariprasad Venugopal, James C. Whisstock, Alex de Marco, Automated cryo-lamella preparation for high-throughput in-situ structural biology, Journal of Structural Biology, Volume 210, Issue 2, 2020 https://doi.org/10.1016/j.jsb.2020.107488.

See CITATION for more details.

Version:

  • 0.3.4

Last updated:

  • 17 May 2024

First released:

  • 04 August 2023

License:

Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 19
  • Forks: 14
  • Issues + PRs: 4

Python versions supported:

Operating system:

Requirements:

  • fibsem>=0.3.3