diff --git a/doc/source/backgroundSubtraction.rst b/doc/source/backgroundSubtraction.rst
index 8f9adc7b89852fe8a46244383cfbb9eb9772fdf8..247f9b1bd436154c87a626191f6532d912598004 100644
--- a/doc/source/backgroundSubtraction.rst
+++ b/doc/source/backgroundSubtraction.rst
@@ -17,8 +17,20 @@ by S.Steinberg (1983).
Background Subtraction in action
+
+Running Background Subtractor plugin in ImageJ macro.
+-----------------------------------------------------
+
+Very often there is a need to process multiple TIFF files. This process can be
+simplify by using following macro.
+
+.. literalinclude:: resources/macros/runBgSubtracktor.ijm
+ :language: java
+ :linenos:
+
+
Algorithm Description
-=====================
+---------------------
-For better algorithm understanding please refer to `Histogram-based background subtractor forImageJ <http://mosaic.mpi-cbg.de/Downloads/BGS_manual.pdf>`_ document.
+For better algorithm understanding please refer to `Histogram-based background subtractor forImageJ <http://sbalzarini-lab.org/Downloads/BGS_manual.pdf>`_ document.
diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
index 7a0515651728728fbfbc81cf535a045969194eb9..331c66029be52237a0ac198a852bef9b185a65ab 100644
--- a/doc/source/changelog.rst
+++ b/doc/source/changelog.rst
@@ -23,4 +23,4 @@ Changelog
.. important::
- For information about previous developments not listed here please refere to `old MosaicSuite site <http://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+ For information about previous developments not listed here please refere to `old MosaicSuite site <http://sbalzarini-lab.org/?q=downloads/imageJ>`_.
diff --git a/doc/source/conf.py b/doc/source/conf.py
index cacd44a4967b84464af6d2785946316d9947afe5..0a8bdef235194eba610686c4761f22ec06e53c45 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -18,7 +18,7 @@
# -- Project information -----------------------------------------------------
project = 'MosaicSuite'
-copyright = '2020, MOSAIC Group, Sbalzarini Lab, mosaic.mpi-cbg.de'
+copyright = '2020, MOSAIC Group, Sbalzarini Lab, sbalzarini-lab.org'
author = 'MOSAIC Group, Sbalzarini Lab'
# The full version, including alpha/beta/rc tags
diff --git a/doc/source/convolutionBesselPSF.rst b/doc/source/convolutionBesselPSF.rst
index 286fa14a3596b239fc35e889e0d6618451e01fdc..fb123af734e55f22fd7edfefcbab2d3a027a08c9 100644
--- a/doc/source/convolutionBesselPSF.rst
+++ b/doc/source/convolutionBesselPSF.rst
@@ -8,5 +8,5 @@ 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>`__.
+For better algorithm understanding please refer to `PDF <https://sbalzarini-lab.org/Downloads/BesselPSFConvolver_manual.pdf>`__.
diff --git a/doc/source/development.rst b/doc/source/development.rst
index cca5fa47bf5321c847b6601edfd43aaca42bf784..505ffd6d02f86b3937be6d0cafa3007fad8e88f5 100644
--- a/doc/source/development.rst
+++ b/doc/source/development.rst
@@ -120,4 +120,50 @@ Running single test within a given test suite:
.. code:: bash
- mvn test -Dtest=CSVTest#testWriteAppend
\ No newline at end of file
+ mvn test -Dtest=CSVTest#testWriteAppend
+
+Documentation
+=============
+
+MosaicSuite documentation is using `Sphinx <https://www.sphinx-doc.org/>`__ documentation generator.
+Documentation is written using reStructuredText markup language (.rxt files) and with Sphinx magic it is easy to convert to HTML or PDF version.
+
+
+Software needed to generate documentation
+-----------------------------------------
+Sphinx requires *make* command, *python* and several libraries. Here are needed steps to install all needed packages using *conda*:
+
+- Create and activate new conda environment:
+
+.. code:: bash
+
+ conda create -n MosaicSuiteDoc
+ conda activate MosaicSuiteDoc
+
+- Install needed libraries:
+
+.. code:: bash
+
+ conda install sphinx
+ conda install recommonmark
+ conda install sphinx_rtd_theme
+
+Generating documentation
+------------------------
+
+Generating documentation is as easy as running *make* command.
+To see all possible targets go to ``doc/`` directory of your cloned MosaicSuite code and run:
+
+.. code:: bash
+
+ make
+
+To generate HTML pages run:
+
+.. code:: bash
+
+ make html
+
+After command is finished in directory ``build/html/`` will be documentation in HTML format ready to deploy server.
+And that's it!
+
diff --git a/doc/source/discreteRegionSampling.rst b/doc/source/discreteRegionSampling.rst
index 4abf5bdc2ed9581d412f87a00bd2b8be8f6fe152..d440c9061d83663475638a7680e849c69229567c 100644
--- a/doc/source/discreteRegionSampling.rst
+++ b/doc/source/discreteRegionSampling.rst
@@ -33,7 +33,7 @@ Options specific for DRS
- **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.
+For detail explanation of these parameters please refere to `PHD thesis <http://sbalzarini-lab.org/docs/Cardinale2013.pdf>`__ desribing theory behind DRS.
Developer Resources
===================
@@ -46,7 +46,7 @@ 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>`__
+ | `PDF <http://sbalzarini-lab.org/docs/Cardinale2013.pdf>`__
*In order to ensure financial support for our project and allow further development of
diff --git a/doc/source/index.rst b/doc/source/index.rst
index b5d5f1e8d395e142143c8ba6ab96a551f4eebd6f..b7c112b96253201e8392352e60566984caf48117 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -5,11 +5,11 @@ MosaicSuite documentation
.. note ::
| This documentation is under development. Some parts might be not valid or incomplete.
- | In a mean time please refere to `old MosaicSuite documentation <http://mosaic.mpi-cbg.de/MosaicToolboxSuite/MosaicToolsuiteTutorials.html>`__.
+ | In a mean time please refere to `old MosaicSuite documentation <http://sbalzarini-lab.org/MosaicToolboxSuite/MosaicToolsuiteTutorials.html>`__.
**MosaicSuite** is a plugin for popular image processing software *ImageJ2* and *Fiji*.
-It provides image-processing algorithms developed at the `MOSAIC group <https://mosaic.mpi-cbg.de>`_.
+It provides image-processing algorithms developed at the `MOSAIC group <https://sbalzarini-lab.org>`_.
The first plugin which is now part of MosaicSuite was a popular 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time. As more plugins have been added, we decided to provide them in a single, coherent package, which will also group them under a common menu point ``Plugins->Mosaic`` in ImageJ2 and Fiji.
diff --git a/doc/source/install.rst b/doc/source/install.rst
index f1c803a084cb8a526d87919ffa940ab15c4c4b41..197c04cf22cec1586267b5e129a1c2c641b0b861 100644
--- a/doc/source/install.rst
+++ b/doc/source/install.rst
@@ -28,4 +28,4 @@ Installation of MosaicSuite plugin
.. important::
If you are using very old Java 6 or because any reason you need to install MosaicSuite manually
- please refere for detailed instructions `old MosaicSuite site <http://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+ please refere for detailed instructions `old MosaicSuite site <http://sbalzarini-lab.org/?q=downloads/imageJ>`_.
diff --git a/doc/source/interactionAnalysis.rst b/doc/source/interactionAnalysis.rst
index 65267bb4eabe84ca6d72ad5ae21148550aed1863..d80fda4426ba2414981349c5d87eb2db64622ffe 100644
--- a/doc/source/interactionAnalysis.rst
+++ b/doc/source/interactionAnalysis.rst
@@ -16,7 +16,7 @@ each other, and the absenceof this means they are independent of each other.
Tutorial
========
-Nice introduction to Interaction Analysis Plugin can be found in this `PDF <http://mosaic.mpi-cbg.de/Downloads/IAPManual.pdf>`_.
+Nice introduction to Interaction Analysis Plugin can be found in this `PDF <http://sbalzarini-lab.org/Downloads/IAPManual.pdf>`_.
For better understanding of output please refer to :ref:`ia-citation` papers.
.. _ia-citation:
diff --git a/doc/source/news.rst b/doc/source/news.rst
index 000dac31010911401a3dc2af9092c4097faa47f7..2066c5de898ca48b805b0bbdc8dfa7e519230d18 100644
--- a/doc/source/news.rst
+++ b/doc/source/news.rst
@@ -10,7 +10,7 @@ News
| *J. Cardinale*
| Unsupervised Segmentation and Shape Posterior Estimation under Bayesian Image Models. PhD thesis, Diss. ETH No. 21026, MOSAIC Group, ETH Zurich, 2013.
- | `PDF <https://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__
+ | `PDF <https://sbalzarini-lab.org/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
@@ -28,7 +28,7 @@ News
| *X. Xiao, V. F. Geyer, H. Bowne-Anderson, J. Howard, and I. F. Sbalzarini.*
| Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets. Med. Image Anal., 32:157–172, 2016.
- | `PDF <https://mosaic.mpi-cbg.de/docs/Xiao2016.pdf>`__
+ | `PDF <https://sbalzarini-lab.org/docs/Xiao2016.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
@@ -42,7 +42,7 @@ News
Currently, we implement Gauss curvature, Mean curvature, and Total Variation (TV) filters.
The only parameters is the number of iterations, i.e., how many passes of the filter should
be applied to the image. Else the filters are parameter free.
- A C++ implementation of these filters is also available `here <https://mosaic.mpi-cbg.de/?q=downloads/curvaturefilters>`__.
+ A C++ implementation of these filters is also available `here <https://sbalzarini-lab.org/?q=downloads/curvaturefilters>`__.
The algorithms implemented in this plug-in are described in:
@@ -50,7 +50,7 @@ News
| Y. Gong and I. F. Sbalzarini.
| Curvature filters efficiently reduce certain variational energies. IEEE Trans. Image Process., 26(4):1786–1798, 2017.
- | `PDF <https://mosaic.mpi-cbg.de/docs/Gong2017.pdf>`__
+ | `PDF <https://sbalzarini-lab.org/docs/Gong2017.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
@@ -72,7 +72,7 @@ News
| Y. Gong and I. F. Sbalzarini.
| Image enhancement by gradient distribution specification. In Proc. ACCV, 12th Asian Conference on Computer Vision, Workshop on Emerging Topics in Image Enhancement and Restoration, pages w7–p3, Singapore, November 2014.
- | `PDF <https://mosaic.mpi-cbg.de/docs/Gong2014.pdf>`__
+ | `PDF <https://sbalzarini-lab.org/docs/Gong2014.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
@@ -80,4 +80,4 @@ News
.. important::
- For information about previous news not listed here please refere to `old MosaicSuite site <https://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+ For information about previous news not listed here please refere to `old MosaicSuite site <https://sbalzarini-lab.org/?q=downloads/imageJ>`_.
diff --git a/doc/source/particleTracker.rst b/doc/source/particleTracker.rst
index 2cb0bc72818ece8ce76fecd77960df9a0b67b365..6780713fcd2007feca469ee1b2ab36d31f4ceeef 100644
--- a/doc/source/particleTracker.rst
+++ b/doc/source/particleTracker.rst
@@ -48,7 +48,7 @@ Citation
| *I. F. Sbalzarini and P. Koumoutsakos*
| Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol., 151(2): 182-195, 2005.
- | `PDF <http://mosaic.mpi-cbg.de/docs/Sbalzarini2005a.pdf>`__
+ | `PDF <http://sbalzarini-lab.org/docs/Sbalzarini2005a.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
diff --git a/doc/source/poissonNoise.rst b/doc/source/poissonNoise.rst
index c4e867b0ecee47ca53b84787f453a34b15004df8..0ea909c9f0cfb963479db13ac601fdb3e667d17f 100644
--- a/doc/source/poissonNoise.rst
+++ b/doc/source/poissonNoise.rst
@@ -15,5 +15,5 @@ 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>`__.
+For better algorithm understanding please refer to `PDF <http://sbalzarini-lab.org/Downloads/PoissonNoise_manual.pdf>`__.
diff --git a/doc/source/psfMeasurement.rst b/doc/source/psfMeasurement.rst
index 12039392e2fb66bb5d3d9a3bb85b211e6d342791..5dd69831a92cf8bf66e77d53f3623cd5b15a7c92 100644
--- a/doc/source/psfMeasurement.rst
+++ b/doc/source/psfMeasurement.rst
@@ -13,5 +13,5 @@ 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>`__
+- **2D** `PDF <https://sbalzarini-lab.org/Downloads/PSFtool.pdf>`__
+- **3D** `PDF <https://sbalzarini-lab.org/Downloads/PSF_measurement_3D.pdf>`__
diff --git a/doc/source/regionCompetition.rst b/doc/source/regionCompetition.rst
index 619218f60eebb150c7451c1d33fbf9c004254779..87b579f083c491814e3bd4d56efb0337bb125f5a 100644
--- a/doc/source/regionCompetition.rst
+++ b/doc/source/regionCompetition.rst
@@ -200,7 +200,7 @@ Citation
| *J. Cardinale, G. Paul, and I. F. Sbalzarini*
| Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012.
- | `PDF <http://mosaic.mpi-cbg.de/docs/Cardinale2012.pdf>`__
+ | `PDF <http://sbalzarini-lab.org/docs/Cardinale2012.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
diff --git a/doc/source/resources/macros/runBgSubtracktor.ijm b/doc/source/resources/macros/runBgSubtracktor.ijm
new file mode 100644
index 0000000000000000000000000000000000000000..8bcd5330a7c4f5bc0da4e66d24b00a57f635d8bc
--- /dev/null
+++ b/doc/source/resources/macros/runBgSubtracktor.ijm
@@ -0,0 +1,61 @@
+// This macro run Background Subtractor plugin from MosaicSuite
+
+
+// ----- USER PARAMETERS
+
+// Provide input directory with images and output directory
+// for saving processed images (if same then input images will be changed!)
+inputDirectory = "/home/gonciarz/1/testImages/"
+outputDirectory="/home/gonciarz/1/results/"
+
+// provide lenght of the sliding window, if set to -1 then plugin will auto-detect
+bgSubtractorSlidingWindowLength=20
+
+// If auto-detection is ON it might happen that plugin is not able to calculate proper length
+// If skipOnFailure is 'false' then popup window will show in such a case (good for interactive operations),
+// if set to 'true' such a case will be only logged and detected lenght will be set to -1
+//
+// Example of log:
+// Macro Options: [length=-1 skipOnFailure ]
+// SkipOnFailure = true
+// Auto-detected length for image a.tif=201
+// Macro Options: [length=-1 skipOnFailure ]
+// SkipOnFailure = true
+// Auto-detected length for image failingImage.tif=-1
+
+skipOnFailure=false
+
+
+// ----- CODE
+
+// Create output (results) directory, if exist nothing happens
+File.makeDirectory(outputDirectory);
+if (!File.exists(outputDirectory)) {
+ exit("Unable to create directory: " + outputDirectory);
+}
+
+
+// Iterate over all 'tif' images in inputDirectory
+images=getFileList(inputDirectory);
+for (i = 0; i < images.length; i++) {
+
+ // Skip if not 'tif' image
+ if (!endsWith(images[i],".tif")) continue;
+
+ // Open current image
+ fullFileName=inputDirectory + "/" + images[i];
+ print("Processing [" + fullFileName + "]");
+ open(fullFileName);
+
+
+ // ----- Run background subtractor ------
+ skipCmd = "";
+ if (skipOnFailure) skipCmd = "skipOnFailure";
+ run("Background Subtractor", "length=" + bgSubtractorSlidingWindowLength + " " + skipCmd);
+
+
+ // Save processed image in output directory and close it
+ save(outputDirectory + "/" + images[i]);
+ close();
+}
+
diff --git a/doc/source/squassh.rst b/doc/source/squassh.rst
index af9a77d575c90302ff5ba88cb8d96a64c7dd9f95..0a97be7f5855767e65ccf7affd32dafa2cb178bd 100644
--- a/doc/source/squassh.rst
+++ b/doc/source/squassh.rst
@@ -24,10 +24,10 @@ 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>`__
+ | `PDF <http://sbalzarini-lab.org/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>`__
+ | `PDF <http://sbalzarini-lab.org/Downloads/SplitBregmanSeg.pdf>`__
Video Tutorial
--------------
@@ -37,11 +37,11 @@ Video Tutorial
.. raw:: html
- <video controls src="http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v" width="720" height="540"></video>
+ <video controls src="http://sbalzarini-lab.org/Downloads/Squassh_video.m4v" width="720" height="540"></video>
.. only:: latex
- `Squassh video tutorial <http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v>`__
+ `Squassh video tutorial <http://sbalzarini-lab.org/Downloads/Squassh_video.m4v>`__
Developer Resources
===================
@@ -54,11 +54,11 @@ 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>`__
+ | `PDF <http://sbalzarini-lab.org/docs/Paul2013a.pdf>`__, `Supplementary Material PDF <http://sbalzarini-lab.org/docs/Paul2013b.pdf>`__, `Matlab Implementation <http://sbalzarini-lab.org/?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>`__
+ | `PDF <http://sbalzarini-lab.org/docs/Rizk2014.pdf>`__, `Supplementary Note PDF <http://sbalzarini-lab.org/docs/Rizk2014a.pdf>`__, `Supplementary Data ZIP <http://sbalzarini-lab.org/docs/Rizk2014_supplement.zip>`__, `Supplementary Video <http://sbalzarini-lab.org/Downloads/Squassh_video.m4v>`__
*In order to ensure financial support for our project and allow further development of