GrotjahnLab / autolamella

Automatic FIBSEM lamella milling

autolamella is a python package for automated cryo-lamella preparation with focused ion beam milling.

Citation

If you find this useful, please cite our work. There is a bioRxiv preprint available at: https://doi.org/10.1101/797506 See CITATION for details.

Software license

This software is released under the terms of the MIT license. There is NO WARRAYNTY either express or implied. See LICENSE for details.

Installation

See INSTALLATION for a more detailed guide.

• Ensure you have Python 3.6 available
• Install Autoscript (a commercial product from FEI) and configure it for use with your FEI microscope
• Download the latest autolamella release wheel from https://github.com/DeMarcoLab/autolamella/releases
• Pip install the wheel file (.whl) into your python environment

Running the program

1. Create/edit the protocol file with details appropriate for your sample. Protocols are YAML files with the format shown by protocol_example.yml (see USER_INPUT.md for more details).
2. Launch the program from the terminal by typing: autolamella path/to/your_protocol.yml
3. Follow the user prompts to interactively select new lamella locations, before beginning the batch ion milling.