bioRxivCell BiologyPreprint
OpenFIBSEM: an application programming interface for easy FIB/SEM automation
P. Cleeve, D. Dierickx, G. Buckley, S. Gorelick, L. Naegele, L. Burne, J. C. Whisstock, A. de Marco
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.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Automated methods for 3D Segmentation of Focused Ion Beam-Scanning Electron Microscopic Images
B. Caffrey, A. V. Maltsev, … S. Subramaniam·bioRxiv·Jan 1, 2019
- Okapi-EM - a napari plugin for processing and analysing cryogenic serial FIB/SEM images
Luı́s M. A. Perdigão, Elaine M. L. Ho, … Michele C. Darrow·Biological ImagingPeer-reviewed·Jan 1, 2023
- mmSIM: An open toolbox for accessible structured illumination microscopy
C. T. Russell, M. Shaw·bioRxiv·Jan 18, 2021
- Image Analysis Tools for Scanning Electron Microscopy
David Shtengel, Gleb E. Shtengel, … Harald F. Hess·bioRxiv·Apr 6, 2026
- A Modular Platform for Streamlining Automated Cryo-FIB Workflows
S. Klumpe, H. K. H. Fung, … J. Mahamid·bioRxiv·May 19, 2021
- Democratising "Microscopi": a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork
M. B. Wincott, A. Jefferson, … R. M. Parton·bioRxiv·May 21, 2020