Imaging

Image analysis using Galaxy

Requirements

Before diving into this topic, we recommend you to have a look at:

Introduction to Galaxy Analyses

Material

Lesson	Slides	Hands-on	Input dataset	Workflows	Galaxy instances
Analyse HeLa fluorescence siRNA screen level level level		tutorial Toggle Dropdown Français 日本語 Español Português العربية And more!	zenodo_link	workflow	instances Galaxy Africa Galaxy@GenOuest Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.no
Introduction to image analysis using Galaxy level level level		tutorial Toggle Dropdown Français 日本語 Español Português العربية And more!	zenodo_link	workflow	instances Galaxy Africa Galaxy@GenOuest Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.no UseGalaxy.org.au
Nucleoli segmentation and feature extraction using CellProfiler	slides Toggle Dropdown Français 日本語 Español Português العربية And more!	tutorial Toggle Dropdown Français 日本語 Español Português العربية And more!		workflow	instances Galaxy Africa Galaxy@GenOuest Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.no
Object tracking using CellProfiler		tutorial Toggle Dropdown Français 日本語 Español Português العربية And more!	zenodo_link	workflow	instances Galaxy Africa Galaxy@GenOuest Street Science UseGalaxy.eu

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/imaging-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.