fibsem

fibsem

a universal api for fibsem control

A universal API for FIBSEM Control, Development and Automation

Overview

OpenFIBSEM 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. OpenFIBSEM 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. OpenFIBSEM is designed to be extensible and can be easily adapted to support new microscopes.

We currently support the TESCAN Automation SDK and ThermoFisher AutoScript. Support for other FIBSEM systems is planned.

Install

Install OpenFIBSEM

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

PyPI (For Users)

pip install fibsem 

Github (For Development)

Clone this repository, and checkout main:

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

Install dependencies and package

cd fibsem
conda create -n fibsem python=3.9 pip
conda activate fibsem
pip install -e .

Napari Plugin

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

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.

Getting Started

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

Recommended: You can start an offline demo microscope by speciying manufacturer: "Demo" in the system.yaml file (fibsem/config/system.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 system.yaml 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.

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 (automated cryo-lamella preparation) in ~150 lines of code

Additional example scripts and notebooks are available.

Projects using OpenFIBSEM

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

Contributing

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

Docs

OpenFIBSEM is a large package with many features. For more detailed documentation, please see the Documentation Website.

Citation

If you find this work useful, please cite:

@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 :)

Version:

  • 0.3.2

Last updated:

  • 01 February 2024

First released:

  • 12 July 2023

License:

Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 21
  • Forks: 8
  • Issues + PRs: 23

Python versions supported:

Operating system:

Requirements:

  • zarr >=2.13.6
  • dask >=2023.3.0
  • tifffile >=2021.7.2
  • numpy >=1.23.5
  • scipy >=1.10.0
  • opencv-python >=4.7.0.72
  • scikit-image >=0.19.3
  • matplotlib >=3.7.0
  • napari >=0.4.17
  • pyqt5 >=5.15.9
  • torch >=2.0.0
  • torchvision >=0.15.1
  • segmentation-models-pytorch >=0.3.2
  • tqdm >=4.65.0
  • pytest >=7.2.2
  • petname >=2.6
  • plotly >=5.14.1
  • kaleido ==0.2.0
  • matplotlib-scalebar >=0.8.1
  • transformers >=4.36.2

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