Image analysis using GalaxyYou can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
- FAIR Data, Workflows, and Research
|Analyse HeLa fluorescence siRNA screen|
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
|Introduction to image analysis using Galaxy|
Nucleoli segmentation and feature extraction using CellProfiler
Object tracking using CellProfiler
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 QuestionsCommon 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.
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.
This material was contributed to by:Leonid KostrykinThomas WollmannSaskia HiltemannAllison CreasonCameron WatsonJean-Karim HérichéBeatriz Serrano-SolanoYi Sun
This material was funded by:
- Thomas Wollmann et al: Workflows for microscopy image analysis and cellular phenotyping