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

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

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:

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

We appreciate if you let us know by email (ilya.belevich -=@=- helsinki.fi) when you cite MIB. This helps us to develop and maintain the program.

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