Imaging

Image analysis using Galaxy

Requirements

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

• Introduction to Galaxy Analyses
• FAIR Data, Workflows, and Research
  • FAIR Bioimage Metadata: tutorial hands-on
  • REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data: tutorial hands-on

Material

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.

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Editorial Board

This material is reviewed by our Editorial Board:

Thomas Wollmann

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Beatriz Serrano-Solano

Laura Cooper

Julia Jakiela

Jean-Karim Hériché

Allison Creason

Saskia Hiltemann

Cameron Watson

Krzysztof Poterlowicz

Katarzyna Kamieniecka

Leonid Kostrykin

Thomas Wollmann

Yi Sun

Funders

This material was funded by:

DASH UK

References

• Thomas Wollmann et al: Workflows for microscopy image analysis and cellular phenotyping