Overview

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

Install OpenFIBSEM

Clone this repository:

$ git clone https://github.com/DeMarcoLab/fibsem.git

Install dependencies and package

$ cd fibsem
$ conda env create -f environment.yml
$ conda activate fibsem
$ pip install -e .

Install autolamella package

Clone this repository:

$ git clone https://github.com/DeMarcoLab/autolamella.git

Install dependencies and package

$ conda activate fibsem
$ cd autolamella
$ pip install -e .
$ pip install pywin32==228
$ conda install -c conda-forge petname

Install AutoScript

You will also need to install AutoScript 4.6+.

Please see the Installation Guide for detailed instructions.

Copy AutoScript /into home/user/miniconda3/envs/fibsem/lib/python3.9/site-packages/

Install TESCAN Automation SDK

Ideally, please install and set up the conda environment first before proceeding to install this SDK

Run the Tescan-Automation-SDK-Installer-3.x.x.exe file

When asked for the python interpretor, select the existing conda environment for FIBSEM, if this python interpretor is not available, see detailed installation guide for a work around

See Installation Guide for full details

Getting started

To run autolamella:

$ conda activate autolamella
$ autolamella

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.