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Genevieve Buckley

[![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/openfibsem-docs/)

## Install

### Recommended Installation Guide

Create a new virtual environment from the Anaconda Prompt terminal:

```bash 
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.

``` bash
conda activate fibsem
autolamella_ui

```

![ui_new](docs/img/ui_new.png)

To launch liftout related methods:

```bash
conda activate fibsem
autoliftout_ui

```

## 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.



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
Recommended Installation Guide
Create a new virtual environment from the Anaconda Prompt terminal:
bash 
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.
``` bash
conda activate fibsem
autolamella_ui
```

To launch liftout related methods:
```bash
conda activate fibsem
autoliftout_ui
```
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.

autolamella

Automatated ion beam milling for cryo-electron microscopy sample preparation.

autolamella

Automatated ion beam milling for cryo-electron microscopy sample preparation.

Documentation¶

Install¶

Recommended Installation Guide¶

Running Autolammela¶

Citation¶

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