****************
User Information
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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 (bftools.zip) 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`

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.

Many other software packages can use Bio-Formats to read and write
microscopy formats (click on the package for further details):

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

