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imaging

Cheminformatics

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:

ToDo

  • data visualization:
    • {% include tool.html id="cardinal_quality_report" label="msi qualitycontrol" %}
    • {% include tool.html id="cardinal_mz_images" label="msi mz images" %}
    • {% include tool.html id="cardinal_spectra_plot" label="msi spectra plot" %}
  • data preprocessing:
    • {% include tool.html id="MALDIquant_preprocessing" label="MALDIquant preprocessing" %}
    • {% include tool.html id="MALDIquant_peak_detection" label="MALDIquant peak detection" %}
    • {% include tool.html id="cardinal_preprocessing" label="msi preprocessing" %}
  • data manipulation:
    • {% include tool.html id="cardinal_filtering" label="msi filtering" %}
    • {% include tool.html id="cardinal_combine" label="msi combine" %}
    • {% include tool.html id="cardinal_data exporter" label="msi data exporter" %}
  • statistical tools:
    • {% include tool.html id="cardinal_segmentation" label="msi segmentation" %}
    • {% include tool.html id="cardinal_classification" label="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 "imaging".

Contributors

References

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