Imaging
Image analysis using Galaxy
Requirements
Before diving into this topic, we recommend you to have a look at:
Material
| Lesson | Slides | Hands-on | Input dataset | Workflows | Galaxy tour | Galaxy instances |
|---|---|---|---|---|---|---|
|
Analyse HeLa fluorescence siRNA screen
level level level
|
tutorial Toggle Dropdown | zenodo_link | workflow | instances | ||
|
Introduction to image analysis using Galaxy
level level level
|
tutorial Toggle Dropdown | zenodo_link | workflow | instances | ||
|
Nucleoli segmentation and feature extraction using CellProfiler
|
slides Toggle Dropdown | tutorial Toggle Dropdown | workflow | instances | ||
|
Object tracking using CellProfiler
|
tutorial Toggle Dropdown | zenodo_link | workflow | instances |
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-trainingNOTE: 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.Maintainers
This material is maintained by:
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:
Thomas Wollmann 
Saskia Hiltemann 
Beatriz Serrano-Solano 
Jean-Karim Hériché 
Yi Sun
References
- Thomas Wollmann et al: Workflows for microscopy image analysis and cellular phenotyping