Commit 8152e8ef authored by gonciarz's avatar gonciarz

Next increment of documentation - small plugins

parent 89cd18b6
......@@ -2,15 +2,23 @@
Background Subtraction
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).
.. 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 <>`_ 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!*
......@@ -62,14 +62,8 @@ html_theme_options = {
html_static_path = ['_static']
# from 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
.. _mosaicsuite-development:
......@@ -26,10 +26,3 @@ The first plugin which is now part of MosaicSuite was a popular 2D/3D single-par
Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
Interaction Analysis
Interaction Analysis (IA)
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
Nice introduction to Interaction Analysis Plugin can be found in this `PDF <>`_.
For better understanding of output please refer to :ref:`ia-citation` papers.
.. _ia-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 <>`__
| *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 <>`__
*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
......@@ -4,13 +4,15 @@ Useful macros
How to run macro
- 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
......@@ -12,4 +12,6 @@ List of plugins delivered in MosaicSuite:
......@@ -164,24 +164,24 @@ Other options
.. |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|
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