Next increment of documentation - basics of DRS

doc/source/convolutionBesselPSF.rst

+================================
+Convolve with 2D Bessel function
+================================
+
+This ImageJ plugin convolves 2D images or movies (image stacks) with a 2D Bessel
+point spread function (PSF).
+
+Algorithm Description and Manual
+================================
+
+For better algorithm understanding please refer to `PDF <https://mosaic.mpi-cbg.de/Downloads/BesselPSFConvolver_manual.pdf>`__.
+

doc/source/discreteRegionSampling.rst

@@ -2,14 +2,52 @@
 Discrete Region Sampling (DRS)
 ==============================
 
-TBD
+Discrete Region Sampling is a sampling version of well known Region Competition algorithm. It can be found in menu ``Segmentation > Discrete Region Sampling``.
+
+.. figure:: resources/discreteRegionSampling/drs.png
+    :scale: 75 %
+    :align: center
+
+    Discrete Region Sampling (DRS) in action
+
+Tutorial
+========
+
+Options shared with Region Competition
+--------------------------------------
+Most of parameters regarding initialization, geometric constrains (fussion, fission, handles) and energies are same as in Region Competition plugin. For their
+description please refere to :ref:`regionCompetition-energy-parameters`.
+
+Options specific for DRS
+------------------------
+- **Number of iterations**
+    Number of iteration (sampling steps) to be performed. Test run of algorithm can be done with quite
+    small number of steps few hundred/thousand but for final run depending on size of a image it should be set to hundred thousands or even millions.
+- **burn-in factor**
+    Fraction of all iterations called **burn-in** phase during which off-boundary probability helps to explore state space.
+    After **burn-in** phase off-boundary probability reduce to 0.
+- off-boundary probability**
+    sets the off-boundary sampling probability
+- **pair proposal**
+    enable mode in which each move corresponds to neighboring pair of particles
+- **biased proposal**
+    enables biased-proposal mode in which in order to propose smoothed shapes
+
+For detail explanation of these parameters please refere to `PHD thesis <http://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__ desribing theory behind DRS.
+
+Developer Resources
+===================
+Source code and helpful information about MosaicSuite development can be found in :ref:`mosaicsuite-development` section.
 
 Citation
 ========
 
 .. admonition:: Citation
 
-    |
+    | *J. Cardinale*
+    | Unsupervised Segmentation and Shape Posterior Estimation under Bayesian Image Models. PhD thesis, Diss. ETH No. 21026, MOSAIC Group, ETH Zurich, 2013.
+    | `PDF <http://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__
+
 
 *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

doc/source/poissonNoise.rst

+=============
+Poisson Noise
+=============
+
+Due to the descrete character of light, images acquired using photon counting devices
+such as CCD cameras suffer from *photon counting noise*: During the exposure time of a
+given time *T*, a photon might or might not hit the sensor (since it is a non-continuous
+event). Such a process can be modeled using a Poisson distribution.
+
+This ImageJ plugin inserts Poisson distributed noise into an image or an imagestack to simulate
+the acquisition of an image. The noise realization is independent for each pixel. The
+distribution parameter *λ* is set to the original intensity value.
+
+
+Algorithm Description and Manual
+================================
+
+For better algorithm understanding please refer to `PDF <http://mosaic.mpi-cbg.de/Downloads/PoissonNoise_manual.pdf>`__.
+

doc/source/psfMeasurement.rst

+=====================
+PSF Measurement 2D/3D
+=====================
+
+With this tool you are able to estimate the PSF of a microscope setup and to compare it
+to the theoretical PSF as calculated from elementary parameters of the microscope and
+the camera.  This serves two purposes:  First, you might want to know whether you
+adjusted your equipment optimally,  and second,  the PSF can be used for image restoration
+purposes (in future versions of the plugin) such as deconvolution.
+
+Algorithm Description and Manual
+================================
+
+For better algorithm understanding please refer to:
+
+- **2D** `PDF <https://mosaic.mpi-cbg.de/Downloads/PSFtool.pdf>`__
+- **3D** `PDF <https://mosaic.mpi-cbg.de/Downloads/PSF_measurement_3D.pdf>`__

doc/source/regionCompetition.rst

@@ -33,6 +33,7 @@ Output of a plugin:
 - **Animated iteration sequence**  Is the evolution of the segmentation produced by the algorithm, can be saved in all imageJ supported formats.
 - **Statistics** Information about found regions like size, coordinates, mean intensity, label etc.
 
+.. _regionCompetition-energy-parameters:
 
 Energy function parameters
 --------------------------