****************
User Information
****************

Every release of Bio-Formats includes a plugin for ImageJ/Fiji, a set of
command line utilities and a MATLAB toolbox.

Using Bio-Formats with ImageJ and Fiji
======================================

The following sections explain the features of Bio-Formats and how to use
it within ImageJ and Fiji:

.. toctree::
    :maxdepth: 1
    :titlesonly:

    imagej/index
    fiji/index
    imagej/features
    imagej/installing
    imagej/load-images
    imagej/managing-memory
    imagej/options

.. seealso::
   :doc:`/formats/options`

Command line tools
==================

The Bio-Formats command line tools provide a complete package
for carrying out a variety of tasks:

.. toctree::
    :titlesonly:
    :includehidden:

    comlinetools/index
    comlinetools/display
    comlinetools/conversion
    comlinetools/xml-validation
    comlinetools/edit
    comlinetools/domainlist
    comlinetools/formatlist
    comlinetools/ijview
    comlinetools/xmlindent
    comlinetools/mkfake
    comlinetools/precompressed

.. seealso::
   :doc:`/formats/options`

Using Bio-Formats in MATLAB/Octave
==================================

The following pages explain how to install and use Bio-Formats in MATLAB or
Octave:

.. toctree::
    :titlesonly:
    :includehidden:

    matlab/index
    octave/index

Third-party applications
========================

Several third-party libraries and applications use Bio-Formats to read and write
imaging formats. All the examples below are maintained outside the Bio-Formats
development release cycle. Any usage question should be raised with their
respective development team.

OMERO
-----

OMERO 5 uses Bio-Formats to read original files from over 140 file formats.
Please refer to the :omero:`OMERO <>` documentation for further
information.


Image server applications
-------------------------

.. toctree::
    :maxdepth: 1
    :titlesonly:

    bisque/index
    ome-server/index


Libraries and scripting applications
------------------------------------

.. toctree::
    :maxdepth: 1
    :titlesonly:

    farsight/index
    i3dcore/index
    imglib/index
    itk/index
    qu-matlab/index


Numerical data processing applications
--------------------------------------

.. toctree::
    :maxdepth: 1
    :titlesonly:

    octave/index
    idl/index
    knime/index
    matlab/index
    visad/index
    r/index


Visualization and analysis applications
---------------------------------------

.. toctree::
    :maxdepth: 1
    :titlesonly:

    imaris/index
    cellprofiler/index
    comstat2/index
    endrov/index
    focalpoint/index
    graphic-con/index
    icy/index
    iqm/index
    micromanager/index
    mipav/index
    qupath/index
    vaa3d/index
    visbio/index
    xuvtools/index