Commit 82129863 authored by gonciarz's avatar gonciarz
Browse files

Migration of server mosaic.mpi-cbg.de -> sbalzarini-lab.org

parent 3d89922c
......@@ -32,5 +32,5 @@ simplify by using following macro.
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.
......@@ -20,4 +20,4 @@ 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>`_.
......@@ -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
......
......@@ -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>`__.
......@@ -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
......
......@@ -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.
......
......@@ -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>`_.
......@@ -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:
......
......@@ -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>`_.
......@@ -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
......
......@@ -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>`__.
......@@ -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>`__
......@@ -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
......
......@@ -9,7 +9,7 @@ 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=-1
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),
......
......@@ -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
......
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