Imaging

Image analysis using Galaxy

Requirements

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

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.
Lesson Slides Hands-on Recordings Input dataset Workflows
Analyse HeLa fluorescence siRNA screen
HeLa
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
Introduction to image analysis using Galaxy
HeLa
Nucleoli segmentation and feature extraction using CellProfiler
Object tracking using CellProfiler
FAIR Bioimage Metadata
fair data management bioimaging
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
fair data management bioimaging

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:

orcid logoThomas Wollmann avatar Thomas Wollmann

Contributors

This material was contributed to by:

Julia Jakiela avatar Julia Jakielaorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoLaura Cooper avatar Laura Cooperorcid logoCameron Watson avatar Cameron WatsonYi Sun avatar Yi Sunorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoAllison Creason avatar Allison Creasonorcid logoThomas Wollmann avatar Thomas WollmannJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamieniecka

Funding

These individuals or organisations provided funding support for the development of this resource

Logo
DASH UK
This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.

References