fibsemOS

A universal API for FIBSEM Control, Development and Automation

Overview

fibsemOS is a Python package for controlling and automating FIB/SEM microscopes. It provides a universal API for FIBSEM control, development and automation, abstracting away the details of the microscope hardware to provide a simple, intuitive interface. The package includes reusable modules for common workflows and operations, and is extensible to support new microscopes.

We currently aim to support ThermoFisher AutoScript, TESCAN Automation SDK, and Zeiss Python API. Support for other FIBSEM systems is planned.

For more information see the website.

Installation

There are several ways to install fibsemOS depending on your application and needs. Requires Python 3.9+.

PyPI (For Users)

pip install fibsem 

Github (For Development)

Clone this repository:

git clone https://github.com/fibsem-os/fibsem-os.git
cd fibsem-os

Install dependencies and package:

conda create -n fibsem python=3.11 pip
conda activate fibsem
pip install -e '.[ui]'

To run:

fibsem-autolamella-ui

Two flags skip the clicks that start every session, for development against a simulator or an instrument you reconnect to all day. --quickstart connects with the default microscope configuration as soon as the window is up; --quickload does that and then reopens the most recent experiment:

fibsem-autolamella-ui --quickload

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):

mkdir pkg
cd pkg
pip download fibsem[ui]

On Support PC: Transfer the pkg directory to the support pc, and then change to the pkg directory

cd pkg
pip install --no-index --find-links . fibsem[ui]

Additional Installation Information

For detailed instructions on installation, and installing the commercial microscope APIs, see Installation Guide.

Getting Started

For a complete walkthrough of the AutoLamella workflow, see the Getting Started Guide.

Getting Started with the API

To get started with the fibsemOS API, see the example/example.py:

You can start an offline demo microscope by specifying 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 plot the results.

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
    sem_image, fib_image = acquire.take_reference_images(microscope, settings.image)

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

Examples

Core Functionality

For examples of core functionality please see:

• example/example_imaging.py: image acquisition
• 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.

Working with experiment data

To read or modify a saved AutoLamella experiment from a plain Python script — no microscope or GUI needed — see the Scripting Guide.

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.

Related Projects and Publications