.. DEFCoN-ImageJ documentation master file, created by
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DEFCoN-ImageJ
=============

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on
fully convolutional neural networks

.. toctree::
   :maxdepth: 1

   instructions
   _javasphinx/packages

This is the ImageJ plugin for the density estimation by fully
convolutional networks (`DEFCoN`_) algorithm, an image processing tool
for fluorescence spot counting. With this plugin, you can use trained
DEFCoN models directly on images from within ImageJ.

Authors
=======

- `Baptiste Ottino <https://github.com/bottino>`_
- `Kyle M. Douglass <https://kmdouglass.github.io>`_

See also
========

- `DEFCoN-ImageJ Wiki`_ - Download site for pre-trained DEFCoN models
- `DEFCoN`_ - Software for training a DEFCoN model
- `ALICA`_ - Automated laser illumination control for Micro-Manager
- `SASS`_ - SMLM acquistion simulation software

Indices and tables
==================

* :ref:`genindex`
* :ref:`search`

.. _DEFCoN-ImageJ Wiki: https://github.com/LEB-EPFL/DEFCoN-ImageJ/wiki
.. _DEFCoN: https://github.com/LEB-EPFL/DEFCoN
.. _ALICA: https://github.com/LEB-EPFL/ALICA
.. _SASS: https://github.com/LEB-EPFL/SASS