autolamella
is a python package for automated cryo-lamella preparation
with focused ion beam milling.
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.
This software is released under the terms of the MIT license. There is NO WARRAYNTY either express or implied. See LICENSE for details.
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
- 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). - Launch the program from the terminal by typing:
autolamella path/to/your_protocol.yml
- Follow the user prompts to interactively select new lamella locations, before beginning the batch ion milling.