fibsem 0.4.1a4
a universal api for fibsem control
License: MIT License
Requires Python: >=3.8

NOTE: This repository is being migrated to a new home at https://github.com/fibsem-os/fibsem-os. This will be kept updated as a mirror for the next few months (until ~September 2025) before being archived. 

# fibsemOS

A universal API for FIBSEM Control, Development and Automation

## Overview

fibsemOS is a Python package for controlling and automating FIB/SEM microscopes. It is designed to be a universal API for FIBSEM control, development and automation. fibsemOS is designed to abstract away the details of the microscope and provide a simple, intuitive interface for controlling the microscope, as well as reuseable modules for common workflows and operations. fibsemOS is designed to be extensible and can be easily adapted to support new microscopes.

We currently support 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.

## Install

### Install fibsemOS

There are several ways to install fibsemOS depending on your application and needs.

#### PyPI (For Users)

```bash
pip install fibsem 
```

#### Github (For Development)

Clone this repository, and checkout main:

```bash
git clone https://github.com/DeMarcoLab/fibsem.git
```

Install dependencies and package

```bash
cd fibsem
conda create -n fibsem python=3.9 pip
conda activate fibsem
pip install -e .[ui]

```

### Offline Installation
For computers with no internet connection, you can download the dependencies on a separate internet connected computer and transfer it to the Support PC (e.g. via USB).

On internet connected PC (Environment should match python version): 
```bash
mkdir pkg
cd pkg
pip download fibsem[ui] autolamella
```
On Support PC:
Transfer the pkg directory to the support pc, and then change to the pkg directory
```bash
cd pkg
pip install --no-index --find-links . fibsem[ui] autolamella
```

#### Napari Plugin

The fibsemOS tools and user interface are also available as a napari plugin:

```bash
pip install napari-openfibsem
```

Or use napari plugin manager

#### Additional Installation Information

For detailed instructions on installation, and installing the commercial microscope APIs, see [Installation Guide](INSTALLATION.md).

## Getting Started

To get started, see the example/example.py:

Recommended: You can start an offline demo microscope by speciying manufacturer: "Demo" in the configuration yaml file (fibsem/config/microscope-configuration.yaml). This will start a demo microscope that you can use to test the API without connecting to a real microscope. To connect to a real microscope, set the ip_address and manufacturer of your microscope in the configuration file or alternatively, you can pass these arguments to utils.setup_session() directly.

This example shows you how to connect to the microscope, take an image with both beams, and then plot.

```python
from fibsem import utils, acquire
import matplotlib.pyplot as plt

def main():

    # connect to microscope
    microscope, settings = utils.setup_session(ip_address="localhost", manufacturer="Demo")

    # take image with both beams
    eb_image, ib_image = acquire.take_reference_images(microscope, settings.image)

    # show images
    fig, ax = plt.subplots(1, 2, figsize=(7, 5))
    ax[0].imshow(eb_image.data, cmap="gray")
    ax[1].imshow(ib_image.data, cmap="gray")
    plt.show()


if __name__ == "__main__":
    main()

```

This example is available as a script in example/example.py.
For more detailed examples, see the Examples sections below.

## Examples

### Core Functionality

For examples of core functionality please see:

- example/example_imaging.py: image acqusition
- example/example_movement.py: stage movement
- example/example_milling.py: drawing patterns and beam milling
- example/autolamella.py: recreation of [AutoLamella V1](https://github.com/DeMarcoLab/autolamella) (automated cryo-lamella preparation) in ~150 lines of code

Additional example scripts and notebooks are available.

## Projects using fibsemOS

We are currently working on a number of projects using fibsemOS. If you are using fibsemOS in your research, please let us know!

- [AutoLamella v2: Automated cryo-lamella preparation](www.github.com/DeMarcoLab/autolamella)
- [Salami: Volume Electron Microscopy](www.github.com/DeMarcoLab/salami)

## Contributing

Contributions are welcome! Please open a pull request or issue.

## Docs

fibsemOS is a large package with many features. For more detailed documentation, please see the [Documentation Website](https://demarcolab.github.io/openfibsem-docs).

## Citation

If you find this work useful, please cite:

```bibtex
@article{CLEEVE2023107967,
title = {OpenFIBSEM: A universal API for FIBSEM control},
journal = {Journal of Structural Biology},
volume = {215},
number = {3},
pages = {107967},
year = {2023},
issn = {1047-8477},
doi = {https://doi.org/10.1016/j.jsb.2023.107967},
url = {https://www.sciencedirect.com/science/article/pii/S1047847723000308},
author = {Patrick Cleeve and David Dierickx and Lucile Naegele and Rohit Kannachel and Lachlan Burne and Genevieve Buckley and Sergey Gorelick and James C. Whisstock and Alex {de Marco}},
keywords = {Focused Ion Beam microscopy, Automation, Python, API, Microscopy, Controller},
abstract = {This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development. OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).}
}
```

enjoy :)