Next increment of documentation - squassh

doc/source/particleTrackerTutorial.rst

@@ -243,6 +243,7 @@ Dynamic models of particle linker
 =============================================
 
 Particle Tracker after detection of particles in individual frames tries to connect them using one of dynamic models:
+
 * **Brownian**: The Brownian model assume a brownian-like motion, so the linking cost is only based on the square of the movement between frames
 * **Constant velocity**: Constant velocity, penalize links that change the velocity of a particle
 * **Straight lines**: Straight lines penalize links that change direction of the particles but not their module, so they can arbitrarily accelerate. (We anyway suggest to start from constant velocity)

doc/source/squassh.rst

@@ -2,7 +2,57 @@
 Squassh
 =======
 
-Documentation under construction
+The Squassh plugin can be used for globally optimal segmentation of piecewise constant regions in 2D and 3D
+images and for object-based co-localization analysis. Globally optimal segmentation is very fast and independent
+of initialization, but it is currently limited to objects with homogeneous (i.e., constant) internal intensity.
+The method can also produce sub-pixel accurate results.
+
+.. figure:: resources/squassh/squassh.png
+    :scale: 75 %
+    :align: center
+
+    Squassh in action
+    *(Picture courtesy of Dr. Magdalena Gonciarz, Mansfeld Lab: HeLa K cells expressing LMNA-GFP)*
+
+Tutorial
+========
+
+Tutorial / workflow
+-------------------
+
+Nice introduction to work with Squassh can be found in following documents:
+
+- | *A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini*
+  | Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014,
+  | `PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014.pdf>`__
+- | *Aurélien Rizk, Grégory Paul, Pietro Incardona, Milica Bugarski, Maysam Mansouri, Axel Niemann, Urs Ziegler, Philipp Berger, Ivo F. Sbalzarini*
+  | An ImageJ/Fiji plugin for segmenting and quantifyingsub-cellular structures in fluorescence microscopy images
+  | `PDF <http://mosaic.mpi-cbg.de/Downloads/SplitBregmanSeg.pdf>`__
+
+Video Tutorial
+--------------
+
+Video tutorial explaining step by step how to install MosaicSuite in Fiji and how to use Squassh.
+
+ .. raw:: html
+
+    <video controls src="http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v" width="720" height="540"></video>
+
 
 Citation
 ========
+
+.. admonition:: Citation
+
+    | *G. Paul, J. Cardinale, and I. F. Sbalzarini*
+    | Coupling image restoration and segmentation: A generalized linear model/Bregman perspective. Int. J. Comput. Vis., 2013.
+    | `PDF <http://mosaic.mpi-cbg.de/docs/Paul2013a.pdf>`__, `Supplementary Material PDF <http://mosaic.mpi-cbg.de/docs/Paul2013b.pdf>`__, `Matlab Implementation <http://mosaic.mpi-cbg.de/?q=downloads/splitBregman>`__
+    |
+    | *A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini*
+    | Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014.
+    | `PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014.pdf>`__, `Supplementary Note PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014a.pdf>`__, `Supplementary Data ZIP <http://mosaic.mpi-cbg.de/docs/Rizk2014_supplement.zip>`__, `Supplementary Video <http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v>`__
+
+
+*In order to ensure financial support for our project and allow further development of
+this software, please cite above publications in all your documents and manuscripts that
+made use of this software. Thanks a lot!*