.. timagetk documentation master file, created by
   sphinx-quickstart on Mon May 30 19:19:49 2016.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. |coord| replace:: S.Ribes, G.Malandain
.. |release| replace:: 1.0.0
.. |licence| replace:: Inria licence
.. |name| replace:: Tissue Image Toolkit

Welcome
*******

**Tissue Image Toolkit** (*timagetk*) is a Python language package dedicated
to image processing of multicellular architectures such as plants or animals,
and is intended for biologists, modelers and computer scientists.

The package provides the following main functionalities (both in 2D and 3D):

.. sidebar:: |name|

   .. image:: _static/logo_timagetk.png
       :width: 70px
       :height: 60px

   Coordination: |coord|

   Teams:
            * Inria-Cirad-Inra `Virtual Plants <https://team.inria.fr/virtualplants/>`_
            * Inria `Morpheme <http://www-sop.inria.fr/morpheme/>`_
            * `Inria Project Lab Morphogenetics <https://team.inria.fr/morphogenetics/>`_

   Stable release: |release|

   Written in: C, Python

   Operaring system: Linux, Mac OS

   Licence: |licence|, no commercial use

* **Linear filtering:** gaussian, gradient, hessian, laplacian, etc.
* **Grayscale mathematical morphology:** erosion, dilation, opening, closing, hat transform, sequential filters, etc.
* **Segmentation:** h-transform, connected-component labeling, watershed, etc.
* **Registration:** rigid, affine and deformable registration, composition of transformations, sequence registration, multi-view fusion etc.
* **Mathematical morphology and computation of features on labeled images:** erosion, dilation, moments, spatial relationships, etc.
* **Temporal tracking based on graph-theory**
* **Unit tests and examples:** see the :ref:`ref_examples`

Thanks to `Python <https://www.python.org/>`_ language these functionalities can
be combined with many other Python libraries such as for example
`NumPy <http://www.numpy.org/>`_ and `SciPy <http://scipy.org/about.html>`_ for scientific
computing or `matplotlib <http://matplotlib.org/>`_ for curve plotting.


Documentation
*************

This is the :ref:`ref_documentation` for |name| version |release|.

To build **timagetk**'s dynamic documentation (`sphinx <http://www.sphinx-doc.org/en/stable/>`_), open a shell prompt and type:

* ``sudo pip install -U Sphinx``

Go to the **timagetk/timagetk/doc/** folder and type:

* ``make html``

Open the file: **timagetk/timagetk/build/html/index.html**


Installation
************

There are many different ways to install |name|, and the best way depends on how you
want to use it and what you already have installed. Order to help you,
the :ref:`ref_installation` instructions have been detailed.


Licence
***********

You can distribute and/or modify |name| under the terms of the |licence|.
Many people have contributed to |name|. Some of the contributors are listed
in the :ref:`ref_credits`. If |name| contributes to a project that leads
to a scientific publication, please acknowledge this
work by :ref:`ref_citing` the project.

.. toctree::
   :maxdepth: 2