fibsemOS documentation

fibsemOS is control software for FIB-SEM microscopes, and AutoLamella is the application built on it for automated cryo-lamella preparation. This guide takes you from an empty computer to a running workflow, one page per task.

Every screenshot in this guide is taken from the application running against its built-in simulator, so what you see here is what you will see on screen. You can follow the whole guide on a laptop with no microscope attached.

Start here

1. Installation: install fibsemOS and make a desktop shortcut.
2. Getting started: set up your microscope configuration and connect for the first time.

Microscope control

The tabs on the Microscope tab, one page each: Image acquisition, Stage movement, Milling, Sample holder, and Fluorescence imaging on an Arctis.

AutoLamella

In a hurry? Your first lamella is the whole run in one page. Otherwise, in the order a session runs: Experiments, Protocols, Overview acquisition, Lamella, Tasks, and Workflows.