Introduction

Overview

This documentation provides a guide for using containerised software environments hosted by the Rosalind Franklin Institute (RFI) for volume electron microscopy (EM) analysis. This work is part of the Collaborative Computational Project for EM project, which aims to support the community by unifying and improving access to important volume EM software.

Quickstart

New to containerisation? We recommend reading our Using Containers page which includes an introduction to the popular container engines Apptainer and Docker.

Requirements

Running the containers requires a working Apptainer or Docker installation. Many volume EM software packages can leverage a GPU to accelerate processing, and some may not function without one (look at for a warning ⚠️ note in the documentation). GPU support is mainly limited to NVIDIA cards on Windows or Linux systems, i.e., users with AMD hardware or macOS may not be able to utilise GPU processing.

Deployed software

Containers have been created for the following software:

• Napari with Clemreg and Empanada Plugins
• Fiji with MoBie
• IMOD
• MiB2

This documentation currently covers the Napari container, with details of the others to be added in future updates.

Info

This documentation is released under a Creative Commons Attribution-Share Alike 4.0 International License (CC BY-SA 4.0). License information for individual software is linked on the relevant page.