external_tools.rst

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