autolamella is a python package for automated cryo-lamella preparation
with focused ion beam milling.
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.
This software is released under the terms of the MIT license. There is NO WARRANTY 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
autolamellarelease 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). - Activate the virtual environment where you have installed
autolamellaand the dependencies (eg: if you are a conda user, open the Anaconda Prompt and use "conda activate my-environment-name" or "source activate my-environment-name", substituting the name of your own virtual environment.) - 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.