Metadata-Version: 2.1
Name: autolamella
Version: 0.2.4
Summary: Automatated ion beam milling for cryo-electron microscopy sample preparation.
Home-page: https://github.com/DeMarcoLab/autolamella
Download-URL: https://github.com/DeMarcoLab/autolamella
Author: Genevieve Buckley
Author-email: Patrick Cleeve <Patrick.Cleeve@monash.edu>
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: fibsem>=0.2.3

[![image](http://img.shields.io/pypi/v/autolamella.svg)](https://pypi.python.org/pypi/autolamella/)

# Overview

AutoLamella is a python package for automated cryo-lamella preparation with focused ion beam milling. It is based on [openFIBSEM](https://github.com/DeMarcoLab/fibsem), and currently supports the [TESCAN Automation SDK](https://www.tescan.com/en/products/automation-sdk/) and [ThermoFisher AutoScript](https://www.tescan.com/en/products/autoscript/). Support for other FIBSEM systems is planned.

## Documentation
[Documentation Site](https://demarcolab.github.io/autolamella/)


## Install

### Recommended Installation Guide

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](docs/img/ui_new.png)

## 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](CITATION.md) for more details.

