Microscopy Image Browser License

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Developed during 2010-2023 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 (GPLv3), 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.
Please note that Microscopy Image Browser was compiled using an Academic license, and its distribution, made by the Electron Microscopy Unit, University of Helsinki is intended only for non-commercial academic research purposes

License for Microscopy Image Browser source code

The source code of Microscopy Image Browser (MIB) is licensed under the GNU General Public License v3 (GPLv3).

By using MIB in MATLAB source code form, you agree to the terms of

Microscopy Image Browser *.m-files are licensed under version 3 of the License, or (at your option) any later version, see the file MIB/licenses/LICENSE_MIB_for_MATLAB or refer to the document below for details.
Initially, the software was licensed under GPLv2, but it has been upgraded to GPLv3 in order to comply with new external packages.

Developed during 2010-2023 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 (MIB)
image segmentation and beyond
Copyright (c) 2010-2023
Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo
http://mib.helsinki.fi

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses


License for compiled application of Microscopy Image Browser

By using the deployed compiled, standalone version of Microscopy Image Browser (MIB), you agree to the following terms: The corresponding license files are also included into the MIB distribution under MIB/licenses directory.

Developed during 2010-2023 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 (MIB)
image segmentation and beyond
Copyright (c) 2010-2023
Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo
http://mib.helsinki.fi
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html.

EXTERNAL PACKAGES

Microscopy Image Browser as a bundle 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 GPLv2,
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
Custom GINPUT Jiro Doke, MathWorks via MATLAB Exchange ModifiedBSD,
2016		 2.82-
Cell migration in scratch wound assays Constantino Carlos Reyes-Aldasoro, City, University of London via MATLAB Exchange GPLv3,
2018		 2.65-
DnD_uifigure: drag & drop functionality for AppDesigner components Xiangrui Li
The Ohio State University		 via MATLAB Exchange MIT,
2020-2023		 2.90-
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 FreeBSD,
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 FreeBSD,
2009		 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 GPLv2,
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 FreeBSD,
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 GPLv2,
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 GPLv2,
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 GPLv2,
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
NRRD NHDR reader and writer Gaetan Rensonnet, Ecole polytechnique federale de Lausanne and Universite catholique de Louvain via MATLAB Exchange CustomBSD
2018		 2.7-
OMERO MATLAB bindings The Open Microscopy Environment OME website GPLv2,
2019		 0.x-2.x
Patch Normals Dirk-Jan Kroon, University of Twente via MATLAB Exchange FreeBSD,
2009		 2.22-
Prettify MATLAB html Harry Dymond, University of Bristol via MATLAB Exchange ModifiedBSD,
2020		 2.83-
Projects:MATLABSlicerExampleModule, to read NRRD format John Melonakos web link GPLv2,
2012		 0.x-2.x
Random Forest MATLAB Abhishek Jaiantilal web link GPLv2,
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
Segment-anything, models Kirillov A, Mintun E, Ravi N, Mao H, Rolland C, Gustafson L, Xiao T, Whitehead S, Berg AC, Lo W-Y, Dollar P, Girshick R, Meta AI web-site Apache-2.0,
2023		 2.90-
Segment-anything for Microscopy, models Archit A, Nair S, Khalid N, Hilt P, Rajashekar V, Freitag M, Gupta S, Dengel A, Ahmed S, Pape C GitHub MIT,
2023		 2.90-
SLIC (Simple Linear Iterative Clustering) Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Susstrunk
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
TEEM.DLL for MATLABSlicerExampleModule Gordon Kindlmann authors' website LGPL plus static linking exception
2012		 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-
VTKPNG.DLL for MATLABSlicerExampleModule Ken Martin, Will Schroeder, Bill Lorensen authors' website ModifiedBSD
2012		 0.x-2.x
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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