****************
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. The list below includes the projects registered as
:imagesc:`Community partners <t/about-the-community-partners-category/33685>` on
the image.sc forum which are known to use Bio-Formats for reading imaging file
formats. The forum is the primary discussion channel for these software projects
and should be used for any questions regarding installation, development or usage:

- :imagesc:`BiofilmQ <tag/biofilmq/1389>`
- :imagesc:`BioFormats.NET <tag/biology-tools/2947>`
- :imagesc:`CellProfiler <tag/cellprofiler/61>`
- :imagesc:`Icy <tag/icy/73>`
- :imagesc:`MIB <tag/mib/1155>`
- :imagesc:`μManager <tag/micro-manager/252>`
- :imagesc:`Orbit <tag/orbit/1071>`
- :imagesc:`OMERO <tag/omero/72>`
- :imagesc:`PolusAI <tag/polusai/2552>`
- :imagesc:`QuPath <tag/qupath/1025>`