Next increment of documentation - small plugins

doc/source/backgroundSubtraction.rst

@@ -2,15 +2,23 @@
 Background Subtraction
 ======================
 
-TBD
+To process images acquired using light microscopy systems, it is often useful to correct
+for inconstant background illumination and artifacts from autofluorescence.
+This software removes nonlinear background. The implemented algorithm is based on the
+assumption that, compared to the background region, object (foreground) regions are small.
+The plugin builds local histograms and assumes the most occuring intensity to be part of
+the background. The plugin is is an alternative to deletion of low frequencies in
+Fourier space or the rolling ball algorithm (ImageJ standard implementation) proposed
+by S.Steinberg (1983).
 
-Citation
-========
+.. figure:: resources/backgroundSubtraction/bg.png
+    :scale: 75 %
+    :align: center
 
-.. admonition:: Citation
+    Background Subtraction in action
 
-    |
+Algorithm Description
+=====================
+
+For better algorithm understanding please refer to `Histogram-based background subtractor forImageJ <http://mosaic.mpi-cbg.de/Downloads/BGS_manual.pdf>`_ document.
 
-*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!*

doc/source/conf.py

@@ -62,14 +62,8 @@ html_theme_options = {
 html_static_path = ['_static']
 
 
-#
-# from sphinx.builders.latex import LaTeXBuilder
-# LaTeXBuilder.supported_image_types = [
-#     'image/svg+xml',
-#     'image/tif',
-#     'image/png',
-#     'image/jpeg'
-# ]
+
+# s
 
 # Change the order of searching img files
 # Thanks to that html will prefere (animated) gifs over png that are used

doc/source/development.rst

+
 .. _mosaicsuite-development:
 
 =======================

doc/source/index.rst

@@ -26,10 +26,3 @@ The first plugin which is now part of MosaicSuite was a popular 2D/3D single-par
    development
    changelog
    macros
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

doc/source/interactionAnalysis.rst

-====================
-Interaction Analysis
-====================
+=========================
+Interaction Analysis (IA)
+=========================
 
-TBD
+The Interaction Analysis plugin (IA) can infer the spatial interaction between two point
+patterns(sets of points).  These points can be locations of molecules, viruses, organelles,
+cells, etc, in 2D or3D. Spatial interaction means the point patterns are correlated with
+each other, and the absenceof this means they are independent of each other.
+
+.. figure:: resources/ia/ia.png
+    :scale: 75 %
+    :align: center
+
+    Interaction Analysis in action
+
+Tutorial
+========
+
+Nice introduction to Interaction Analysis Plugin can be found in this `PDF <http://mosaic.mpi-cbg.de/Downloads/IAPManual.pdf>`_.
+For better understanding of output please refer to :ref:`ia-citation` papers.
+
+.. _ia-citation:
 
 Citation
 ========
 
 .. admonition:: Citation
 
-    |
+    | *J. A. Helmuth, G. Paul, and I. F. Sbalzarini*
+    | Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11:372, 2010.
+    | `PDF <http://www.biomedcentral.com/1471-2105/11/372>`__
+
+    | *A. Shivanandan, A. Radenovic, and I. F. Sbalzarini*
+    | MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis. BMC Bioinformatics, 14:349, 2013
+    | `PDF <http://www.biomedcentral.com/1471-2105/14/349/>`__
 
 *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/macros.rst

@@ -4,13 +4,15 @@ Useful macros
 
 How to run macro
 ----------------
-
-TBD
-
+- To use macro from file run ``Plugins > Macro > Run..`` and choose correct file with your macro.
+- To create (or paste copied) macro run ``Plugins > New > Macro`` and after editing click ``Run`` button.
 
 Convert CZI files to TIFF
 -------------------------
 
+Very often there is a need to convert a lot of CZI files to TIFF files. This process can be
+simplify by using following macro. Edit your input and output directory and run macro!
+
 .. literalinclude:: resources/macros/ConvertCZItoTIFF.ijm
     :language: java
     :linenos:

doc/source/plugins.rst

@@ -12,4 +12,6 @@ List of plugins delivered in MosaicSuite:
     interactionAnalysis
     backgroundSubtraction
     discreteRegionSampling
-
+    psfMeasurement
+    poissonNoise
+    convolutionBesselPSF

doc/source/regionCompetition.rst

@@ -164,24 +164,24 @@ Other options
 Examples
 ========
 
-    .. |e1| image:: resources/regionCompetition/nucleis.jpg
+    .. |e1| image:: resources/regionCompetition/nucleisInput.jpg
             :width: 45%
-    .. |e2| image:: resources/regionCompetition/nucleis.gif
+    .. |e2| image:: resources/regionCompetition/nucleis.*
             :width: 45%
 
     .. |e3| image:: resources/regionCompetition/icecream5_410x410.jpg
             :width: 45%
-    .. |e4| image:: resources/regionCompetition/icecream5_rs.gif
+    .. |e4| image:: resources/regionCompetition/icecream5_rs.*
             :width: 45%
 
-    .. |e5| image:: resources/regionCompetition/endo.jpg
+    .. |e5| image:: resources/regionCompetition/endoInput.jpg
             :width: 45%
-    .. |e6| image:: resources/regionCompetition/endo.gif
+    .. |e6| image:: resources/regionCompetition/endo.*
             :width: 45%
 
     .. |e7| image:: resources/regionCompetition/uc_data.jpg
             :width: 45%
-    .. |e8| image:: resources/regionCompetition/Dev_res_rs.gif
+    .. |e8| image:: resources/regionCompetition/Dev_res_rs.*
             :width: 45%
 
     |e1| |e2|