Cloud based bioimage analysis course overview

Prerequisites
Before starting this lesson, you should be familiar with:

Basic knowledge of desktop based image analysis tools, e.g. Fiji

Basic shell command-line skills

Learning Objectives
After completing this lesson, learners should be able to:

Execute cloud based interactive biomage analysis tools

Execute and manage cloud based batch analysis workflows

Use bioimage tool containers

Create bioimage tool containers

Motivation

Cloud-based bioimage analysis offers several advantages, including:

access to high-end hardware: multi-core, large RAM, GPUs
access to preinstalled software
reproducibility: different people running same software on same hardware
scalability: spawn various computational jobs in parallel

Concept map

graph TD; C("Client computer(s)") -->|"shell, browser"| CR("Cloud resource\n\n(Google Colab, Slurm cluster,\nVirtual desktop, Galaxy, ...)") CR --- S("Software") CR --- H("Hardware")

Figure

Course overview

The material for this course consists of the following training modules:

As usual, each training module contains several activities that can be executed on various compute platforms. As a trainer, it is necessary to familiarise yourself with the material before and decide which activities to teach. It is also highly recommended to consider our TEACHING TIPS.

Cloud based bioimage anlaysis

In this document we are attempting to review the currently available options for conducting cloud based bioimage analysis.

Follow-up material

Recommended follow-up modules:

Cloud based interactive analysis

Learn more:

Docker for beginers

BARD Desktop

Galaxy training network