index-imaging.md

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Welcome to our Imaging flavour of UseGalaxy.eu -- a webserver to process and analyse (biomedical) images.

1. TOC {:toc}

Get started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour{:target="_blank"} through Galaxy's user interface.

Want to learn about imaging? Check our tutorials or take one of our guided tour:

TODO

Check also the standard but customizable workflows available there.

Tools

Several tools are integrated in this custom Galaxy instance. They were chosen for their use in exploitation of chemical data:

• data visualization:
  • msi qualitycontrol
  • msi mz images
  • msi spectra plot
• data preprocessing:
  • MALDIquant preprocessing
  • MALDIquant peak detection
  • msi preprocessing
• data manipulation:
  • msi filtering
  • msi combine
  • msi data exporter
• statistical tools:
  • msi segmentation
  • msi classification

Tutorials

ToDo

Workflows

To orchestrate tools and help users with their analyses, several workflows are available. They formally orchestrate tools in a defined order and with defined parameters, but they are customizable (tools, order, parameters).

The workflows are available in the Shared Workflows, with the label "cheminformatics".

Contributors

• Biomedical Computer Vision Group lead by Karl Rohr
• Thomas Wollmann
• Greg von Kuster

References

{% bibliography --cited --prefix index-metagenomics --group_by none %}