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External Software and OMERO

Here we describe how to use third party tools to analyze data stored in OMERO. We provide installation instructions, step-by-step workflow either to use the User Interface or the API of those tools.

|cellprofiler|_ :doc:`cellprofiler/docs/index`  
|fiji|_ :doc:`fiji/docs/index`  
|ilastik|_ :doc:`ilastik/docs/index`  
|orbit|_ :doc:`orbit/docs/index`  
|qupath|_ :doc:`qupath/docs/index`  
|tm|_ :doc:`trackmate/docs/index`  
.. toctree::
    :maxdepth: 1
    :hidden:

    cellprofiler/docs/index
    fiji/docs/index
    ilastik/docs/index
    orbit/docs/index
    qupath/docs/index
    trackmate/docs/index