Microscopy Image Browser License
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Contents
Developed during 2010-2021 by
Core developer:
Ilya Belevich
Developers:
Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo
Electron Microscopy Unit
Institute of Biotechnology
PO Box 56 (Viikinkaari 9)
00014, University of Helsinki
Finland
Microscopy Image Browser source code
MIB in MATLAB source code form is licensed under the GNU General Public License (GPL2), see GPL license of Microscopy Image Browser source code section below.Microscopy Image Browser as standalone version
The deployed application is governed by the MathWorks MCR license and applicable parts of The MathWorks, Inc. Software License Agreement.Using the Microscopy Image Browser deployed application for commercial purposes is prohibited.
License for Microscopy Image Browser source code
Microscopy Image Browser (MIB)
image segmentation and beyond
Copyright (c) 2010-2020
Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo
http://mib.helsinki.fi
Source code of Microscopy Image Browser (MIB) is licensed under the GNU General Public License v2.
By using MIB in MATLAB source code form, you agree to the terms of
- the GNU General Public License, version 2 (link)
- the licenses of external packages (See the section below for details)
- the following disclaimer:
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. MATHWORKS AND ITS LICENSORS ARE EXCLUDED FROM ALL LIABILITY FOR DAMAGES OR ANY OBLIGATION TO PROVIDE REMEDIAL ACTIONS.
License for compiled application of Microscopy Image Browser
By using the compiled, standalone version of Microscopy Image Browser (MIB)</b, you agree to the terms of
- the disclaimer below;
- the Matlab Compiler Runtime (MCR) libraries license;
- applicable parts of the MathWorks, Inc. Software License Agreement;
- as Microscopy Image Browser (MIB) was compiled using Academic license, its usage for for commercial purposes is prohibited
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. MATHWORKS AND ITS LICENSORS ARE EXCLUDED FROM ALL LIABILITY FOR DAMAGES OR ANY OBLIGATION TO PROVIDE REMEDIAL ACTIONS.
The corresponding license files are also included into the MIB distribution under techdoc directory.
EXTERNAL PACKAGES
Source code of Microscopy Image Browser is licensed under the GPL, with exceptions for plugins and other components. This section lists the license under which additional components are released. See also the Acknowledgements section
Abbreviations:
- FreeBSD, Berkeley Software Distribution, 2-clause license, GPL compatible
- GPL, GNU General Public License, version 2
- GPL3, GNU General Public License, version 3
- ModifiedBSD, Berkeley Software Distribution, 3-clause license, GPL compatible
- MIT, a free software license originating at the Massachusetts Institute of Technology, GPL compatible
- CC BY-ND 3.0, Attribution-NoDerivs 3.0 Unported
- ND, no data
Name | Author(s) | Contact | License, Year | MIB version |
Accurate Fast Marching | Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2011 |
0.x-2.x |
ANISODIFF | Peter Kovesi | web site | MIT, 2000-2002 |
0.x-2.x |
Bio-Formats | Melissa Linkert, Curtis Rueden et al. | web site | GPL, 2002-2013 |
0.x-2.x |
bwdistsc, 3D Euclidean distance transform for variable data aspect ratio | Yuriy Mishchenko, Toros University | via Matlab Exchange | FreeBSD, 2007-2013 |
0.x-2.x |
Cell migration in scratch wound assays | Constantino Carlos Reyes-Aldasoro, City, University of London | via Matlab Exchange | GPL3, 2018 |
2.65- |
Drag & Drop functionality for JAVA GUI components | Maarten van der Seijs Delft University of Technology, the Netherlands |
via Matlab Exchange | FreeBSD, 2015 |
2.61- |
DrawRegionBoundaries | Peter Kovesi Centre for Exploration Targeting, School of Earth and Environment, The University of Western Australia |
author's website | MIT, 2013 |
0.x-2.x |
drifty_shifty_deluxe | Joshua D. Sugar Sandia National Laboratories, Livermore, CA |
via Matlab Exchange | Custom, 2014 |
0.x-2.x |
Export_fig | Oliver Woodford and Yair Altman | via Matlab Exchange | ModifiedBSD, 2014-2015 |
0.x-2.x |
Extrema functions | Carlos Adrian Vargas Aguilera, Universidad de Guadalajara | via Matlab Exchange | ND, 2006-2007 |
0.x-1.x |
Fast 3D/2D Region Growing (MEX) | Christian Wuerslin, Stanford University | via Matlab Exchange | ModifiedBSD, 2013-2015 |
0.x-2.x |
Fast/Robust Template Matching
used in MIB 1.22 and earlier
|
Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2009-2011 |
0.x-1.22 |
FindJObj - find java handles of Matlab graphic objects | Yair Altman | via Matlab Exchange | FreeBSD, 2007-2013 |
0.x-2.x |
fstack - extended depth-of-field image | Said Pertuz, Universitat Rovira i Virgili, Tarragona, Spain | via Matlab Exchange | ModifiedBSD, 2013 |
2.51- |
Hardware accelerated 3D viewer for MATLAB | Jean-Yves Tinevez, Institut Pasteur | via Matlab Exchange | FreeBSD, 2011 |
0.x-2.x |
Hessian based Frangi Vesselness filter | Marc Schrijver and Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2001-2009 |
0.x-2.x |
Highly portable JSON-input parser | Nedialko | via Matlab Exchange | GPL, 2013 |
0.x-2.x |
HistThresh toolbox | Antti Niemistö, Tampere University of Technology, Finland | Github | GPLv3, 2014 |
2.51 - |
IceImarisConnector | Aaron C. Ponti, ETH Zurich | web link | GPL, 2013 |
0.x-2.x |
Image Edge Enhancing Coherence Filter | Dirk-Jan Kroon, Pascal Getreuer University of Twente | via Matlab Exchange | FreeBSD, 2009 |
0.x-1.x |
Image Measurement Utility | Jan Neggers, Eindhoven Univeristy of Technology | via Matlab Exchange | FreeBSD, 2009-2014 |
1.x-2.x |
ImageViewer | Jiro Doke, Mathworks | via Matlab Exchange | ModifiedBSD, 2010 |
0.x-2.x |
ImClipboard | Jiro Doke, MathWorks | via Matlab Exchange | ModifiedBSD, 2010 |
0.x-2.x |
ImGaussian | Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2009 |
0.x-2.x |
Local Normalization | Guanglei Xiong at Tsinghua University, Beijing | via Matlab Exchange | ND, 2005 |
0.x-1.x |
MatGeom | David Legland, INRA, France | GitHub | FreeBSD, 2011- |
2.3- |
MatTomo, a part of PEET | Boulder Laboratory for 3-D Electron Microscopy of Cells | web site | GPL, 2006-2010 |
0.x-2.x |
MAXFLOW/MINCUT algorithm v2.22 | Yuri Boykov, University of Western Ontario and Vladimir Kolmogorov, Microsoft research, Cambridge | web site | GPL, 2001-2014 |
0.x-2.x |
MAXFLOW/MINCUT Matlab wrapper | Michael Rubinstein, Google | via Matlab Exchange | FreeBSD, 2008 |
0.x-2.x |
Membrane detection with Random Forest | Verena Kaynig, Harvard School of Engineering and Applied Sciences | web link | GPL, 2010 |
0.x-2.x |
MIJ: Running ImageJ and Fiji within Matlab | Daniel Sage, Dimiter Prodanov, Jean-Yves Tinevez and Johannes Schindelin, EPFL Lausanne | via Matlab Exchange | ModifiedBSD, 2012-2017 |
2.6- |
MTOC++ | Martin Drohmann (Universit?t M?nster), Daniel Wirtz (Universit?t Stuttgart) | via Matlab Exchange | FreeBSD, 2011-2013 |
0.x-2.x |
NRRD Format File Reader | Jeff Mather, the MathWorks, Inc. | via Matlab Exchange | ModifiedBSD, 2012 |
0.x-2.x |
OMERO Matlab bindings | The Open Microscopy Environment | OME website | GPL, 2019 |
0.x-2.x |
Patch Normals | Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2009 |
2.22- |
Projects:MATLABSlicerExampleModule, to read NRRD format | John Melonakos | web link | GPL, 2012 |
0.x-2.x |
Random Forest Matlab | Abhishek Jaiantilal | web link | GPL, 2012 |
0.x-2.x |
Region Adjacency Graph (RAG) | David Legland, INRA, France | via Matlab Exchange | FreeBSD, 2007-2013 |
0.x-2.x |
RegionProps3 | Chaoyuan Yeh | via Matlab Exchange | FreeBSD, 2014 |
0.x-2.x |
Render | Dirk-Jan Kroon, Focal Machine Vision en Optical Systems | via Matlab Exchange | FreeBSD, 2008-2011 |
1.x-2.x |
Render RGB text over RGB or Grayscale Image | Davide Di Gloria, Universita di Genova | via Matlab Exchange | FreeBSD, 2010 |
0.x-2.x |
SLIC (Simple Linear Iterative Clustering) | Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi,
Pascal Fua, and Sabine S?sstrunk Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland |
authors' website | ModifiedBSD, 2015 |
0.x-2.x |
STLWRITE | Sven Holcombe, University of Michigan | via Matlab Exchange | FreeBSD, 2008-2015 |
1.x-2.x |
STRUCT2XML | Wouter Falkena, Delft University of Technology | via Matlab Exchange | FreeBSD, 2010 |
0.x-2.x |
UIGETFILE_N_DIR | Tiago / Peugas | via Matlab Exchange | FreeBSD, 2011 |
2.6- |
VIEW3D | Torsten Vogel | via Matlab Exchange | FreeBSD, 1999 |
0.x-2.x |
VIOLIN | Holger Hoffmann | via Matlab Exchange | FreeBSD, 2015 |
2.65- |
XLWRITE: Generate XLS(X) files without Excel on Mac/Linux/Win | Alec de Zegher, NV Bekaert SA | via Matlab Exchange | FreeBSD, 2013 |
2.1-2.x |
XLSWRITE (improved) | Barry Dillon, AON Insurance Brokers | via Matlab Exchange | FreeBSD, 2010 |
0.x-2.x |
XML2STRUCT | Wouter Falkena, Delft University of Technology | via Matlab Exchange | FreeBSD, 2010 |
0.x-2.x |
Some icons | Icons8.com | website | CC BY-ND 3.0, 2018 |
2.22- |
HOW TO CITE
In November 2015 paper describing Microscopy Image Browser was accepted for publication in PLOS Biology,
please cite it whenever referring to the software (the reference will be updated as soon as the article is published):
Microscopy Image Browser: A platform for segmentation and analysis of
multidimensional datasets
I. Belevich, M. Joensuu, D. Kumar, H. Vihinen and E. Jokitalo
PLOS Biology, PLoS Biology 2016 Jan 4;14(1):e1002340. doi: 10.1371/journal.pbio.1002340
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