Microscopy Image Browser License
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Contents
Developed during 2010-2015 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
GPL license of Microscopy Image Browser
Microscopy Image Browser (MIB) a handy tool for image management
Copyright (c) 2010-2015
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 < http://www.gnu.org/licenses/gpl-2.0.html GNU General Public License> as published by the Free Software Foundation; either version 2 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, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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: * FreeBSD, Berkeley Software Distribution, 2-clause license, GPL compatible * GPL, GNU General Public License, version 2 * ModifiedBSD, Berkeley Software Distribution, 3-clause license, GPL compatible * MIT, a free software license originating at the Massachusetts Institute of Technology, GPL compatible * ND, no data
| Name | Author(s) | Contact | License, Year |
| Accurate Fast Marching | Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2011 |
| ANISODIFF | Peter Kovesi | web site | MIT, 2000-2002 |
| Bio-Formats | Melissa Linkert, Curtis Rueden et al. | web site | GPL, 2002-2013 |
| bwdistsc, 3D Euclidean distance transform for variable data aspect ratio | Yuriy Mishchenko, Toros University | via Matlab Exchange | FreeBSD, 2007-2013 |
| DrawRegionBoundaries | Peter Kovesi Centre for Exploration Targeting, School of Earth and Environment, The University of Western Australia |
author's website | MIT, 2013 |
| drifty_shifty_deluxe | Joshua D. Sugar Sandia National Laboratories, Livermore, CA |
via Matlab Exchange | Custom, 2014 |
| Export_fig | Oliver Woodford and Yair Altman | via Matlab Exchange | ModifiedBSD, 2014-2015 |
| Extrema functions | Carlos Adrian Vargas Aguilera, Universidad de Guadalajara | via Matlab Exchange | ND, 2006-2007 |
| Fast 3D/2D Region Growing (MEX) | Christian Wuerslin, Stanford University | via Matlab Exchange | ModifiedBSD, 2013-2015 |
| Fast/Robust Template Matching
used in MIB 1.22 and earlier
|
Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2009-2011 |
| FindJObj - find java handles of Matlab graphic objects | Yair Altman | via Matlab Exchange | FreeBSD, 2007-2013 |
| Hardware accelerated 3D viewer for MATLAB | Jean-Yves Tinevez, Institut Pasteur | via Matlab Exchange | FreeBSD, 2011 |
| Hessian based Frangi Vesselness filter | Marc Schrijver and Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2001-2009 |
| Highly portable JSON-input parser | Nedialko | via Matlab Exchange | FreeBSD, 2009 |
| IceImarisConnector | Aaron C. Ponti, ETH Zurich | web link | GPL, 2013 |
| Image Edge Enhancing Coherence Filter | Dirk-Jan Kroon, Pascal Getreuer University of Twente | via Matlab Exchange | FreeBSD, 2009 |
| Image Measurement Utility | Jan Neggers, Eindhoven Univeristy of Technology | via Matlab Exchange | FreeBSD, 2009-2014 |
| ImageViewer | Jiro Doke, Mathworks | via Matlab Exchange | ModifiedBSD, 2010 |
| ImClipboard | Jiro Doke, MathWorks | via Matlab Exchange | ModifiedBSD, 2010 |
| ImGaussian | Dirk-Jan Kroon, University of Twente | via Matlab Exchange | FreeBSD, 2009 |
| Local Normalization | Guanglei Xiong at Tsinghua University, Beijing | via Matlab Exchange | ND, 2005 |
| MatTomo, a part of PEET | Boulder Laboratory for 3-D Electron Microscopy of Cells | web site | GPL, 2006-2010 |
| MAXFLOW/MINCUT algorithm v2.22 | Yuri Boykov, University of Western Ontario and Vladimir Kolmogorov, Microsoft research, Cambridge | web site | GPL, 2001-2014 |
| MAXFLOW/MINCUT Matlab wrapper | Michael Rubinstein, Google | via Matlab Exchange | FreeBSD, 2008 |
| Membrane detection with Random Forest | Verena Kaynig, Harvard School of Engineering and Applied Sciences | web link | GPL, 2010 |
| MTOC++ | Martin Drohmann (Universität Münster), Daniel Wirtz (Universität Stuttgart) | via Matlab Exchange | FreeBSD, 2011-2013 |
| NRRD Format File Reader | Jeff Mather, the MathWorks, Inc. | via Matlab Exchange | ModifiedBSD, 2012 |
| Projects:MATLABSlicerExampleModule, to read NRRD format | John Melonakos | web link | GPL, 2012 |
| Random Forest Matlab | Abhishek Jaiantilal | web link | GPL, 2012 |
| Region Adjacency Graph (RAG) | David Legland, INRA, France | via Matlab Exchange | FreeBSD, 2007-2013 |
| RegionProps3 | Chaoyuan Yeh | via Matlab Exchange | FreeBSD, 2014 |
| Render | Dirk-Jan Kroon, Focal Machine Vision en Optical Systems | via Matlab Exchange | FreeBSD, 2008-2011 |
| Render RGB text over RGB or Grayscale Image | Davide Di Gloria, Universita di Genova | via Matlab Exchange | FreeBSD, 2010 |
| SLIC (Simple Linear Iterative Clustering) | Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi,
Pascal Fua, and Sabine Süsstrunk Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland |
authors' website | ModifiedBSD, 2015 |
| STLWRITE | Sven Holcombe, University of Michigan | via Matlab Exchange | FreeBSD, 2008-2015 |
| STRUCT2XML | Wouter Falkena, Delft University of Technology | via Matlab Exchange | FreeBSD, 2010 |
| VIEW3D | Torsten Vogel | via Matlab Exchange | FreeBSD, 1999 |
| XLSWRITE (improved) | Barry Dillon, AON Insurance Brokers | via Matlab Exchange | FreeBSD, 2010 |
| XML2STRUCT | Wouter Falkena, Delft University of Technology | via Matlab Exchange | FreeBSD, 2010 |
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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