A univseral API for FIBSEM Control, Development and Automation

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.

Clone this repository, and checkout v0.2-stable:

$ git clone https://github.com/DeMarcoLab/fibsem.git
$ git checkout origin/v0.2-stable

Install dependencies and package

$ cd fibsem
$ conda env create -f environment.yml
$ conda activate fibsem
$ pip install -e .

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

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.

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

• Take an Electron Beam image with autocontrast...

AutoScript

    from autoscript_sdb_microscope_client import SdbMicroscopeClient
    from autoscript_sdb_microscope_client.structures import GrabFrameSettings, RunAutoCbSettings

    # connect to microscope
    microscope = SdbMicroscopeClient()
    microscope.connect("10.0.0.1")

    # set the active view
    microscope.imaging.set_active_view(1)

    # set frame settings
    frame_settings = GrabFrameSettings(
        resolution="1536x1024",
        dwell_time=1e-6,
    )

    # set hfw
    microscope.beams.electron_beam.horizontal_field_width.value = 150e-6

    # autocontrast
    cb_settings = RunAutoCbSettings(
        method="MaxContrast",
        resolution="768x512",  
        number_of_frames=5,
    )
    microscope.auto_functions.run_auto_cb(cb_settings)

    # grab frame
    eb_image = microscope.imaging.grab_frame(frame_settings)

OpenFIBSEM

from fibsem import utils, acquire
from fibsem.structures import BeamType, ImageSettings

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

# set imaging settings
image_settings = ImageSettings(
        hfw=150e-6, 
        resolution=(1536, 1024),
        dwell_time=1e-6, 
        autocontrast=True, 
        beam_type=BeamType.ELECTRON)

# take electron image
eb_image = acquire.new_image(microscope, image_settings)

The example directory contains the following applications:

Autolamella (autolamella.py)

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

Volume Microscopy (slice_and_view.py)

Recreation of a volume microscopy workflow (slice and view) in ~50 lines of code.

Lithography (lithography.py)

Milling of a grayscale lithography profile using a bitmap pattern.

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

• AutoLamella v2: Automated cryo-lamella preparation
• AutoLiftout: Automated cryo-liftout
• Salami: Volume Electron Microscopy
• Vulcan: Grayscale FIB Lithography

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

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

@article {Cleeve2022.11.01.514681,
 author = {Cleeve, Patrick and Dierickx, David and Buckley, Genevieve and Gorelick, Sergey and Naegele, Lucile and Burne, Lachlan and Whisstock, James C and de Marco, Alex},
 title = {OpenFIBSEM: an application programming interface for easy FIB/SEM automation},
 elocation-id = {2022.11.01.514681},
 year = {2022},
 doi = {10.1101/2022.11.01.514681},
 publisher = {Cold Spring Harbor Laboratory},
 abstract = {Automation in microscopy is the key to success in long and complex experiments. Most microscopy manufacturers provide Application Programming Interfaces (API) to enable communication between a user-defined program and the hardware. Although APIs effectively allow the development of complex routines involving hardware control, the developers need to build the applications from basic commands. Here we present a Software Development Kit (SDK) for easy control of Focussed Ion Beam Scanning Electron Microscopes (FIB/SEM) microscopes. The SDK, which we named OpenFIBSEM consists of a suite of building blocks for easy control that simplify the development of complex automated workflows.Competing Interest StatementThe authors have declared no competing interest.},
 URL = {https://www.biorxiv.org/content/early/2022/11/06/2022.11.01.514681},
 eprint = {https://www.biorxiv.org/content/early/2022/11/06/2022.11.01.514681.full.pdf},
 journal = {bioRxiv}
}

enjoy :)