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 VolumeEM (CCP-volumeEM) project, which aims to support the volume EM community by unifying and improving access to important software.

Quickstart

If you are completely new to EM software or have little computing experience in general, you may like to view our Using Volume EM Containers Introductory Slides (particularly relevant if you are taking part in a DAaaS training session). Otherwise, if you are unfamiliar with containerisation or need a refresher, we recommend reading our Using Containers page, which includes an introduction to the popular container engines Apptainer and Docker.

System Administrators

For system administrators, research software engineers and other IT technicians, there is a one-page setup guide for running the containerised software.

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.