Acknowledgements

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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

Special thanks come to

Konstantin Kogan, Institute of Biotechnology, University of Helsinki for help with Mac OS.
Radhakrishna Achanta, Ecole Polytechnique Fédérale de Lausanne (EPFL) for the mex code for SLIC supervoxels and superpixels
David Legland, INRA, France for modification of the Region Adjacency Graph (imRAG) function for detection of indices between watershed regions
John Heumann, The Boulder Laboratory For 3-D Electron Microscopy of Cells for help with Mattomo
Tom Boissonnet, EMBL for extensive testing

Microscopy Image Browser team would like to acknowledge the User Community of Matlab-Central and the authors whose code was used during MIB development. Microscopy Image Browser adapts partially or completely codes from the following sources:

Inspired by IMAGEVIEWER by Jiro Doke, MathWorks 2010
Documentation done with MTOC++ - Doxygen filter for Matlab and tools written by Martin Drohmann (Universität Münster) and Daniel Wirtz (Universität Stuttgart), 2011-2013
Accurate Fast Marching function by Dirk-Jan Kroon, University of Twente, 2011 is utilized in the Membrane Click Tracker tool
ANISODIFF function written by Peter Kovesi, 2000-2002
BIO-FORMATS by Melissa Linkert, Curtis Rueden et al. 2002-2013
BWDISTSC for 3D Euclidean distance transform for variable data aspect ratio written by Yuriy Mishchenko, Toros University, 2007-2013
DIPLIB is a platform independent scientific image processing library written in C developed by Quantitative Imaging Group at the Faculty of Applied Sciences, Delft University of Technology. When installed, Microscopy Image Browser can use several additional methods for anisotropic diffusion filtering available from DipLib
DRAWREGIONBOUNDARIES a function to draw boundaries of labeled regions in an image, written by Peter Kovesi Centre for Exploration Targeting, School of Earth and Environment, The University of Western Australia, 2013.
DRIFTY_SHIFTY_DELUXE, written by Joshua D. Sugar, Sandia National Laboratories, Livermore, CA (2014); part of code from this function was adopted in mib_calcShifts.m
EXPORT_FIG function to add measurements to snapshots is written by Oliver Woodford and Yair Altman
EXTREMA functions by Carlos Adrian Vargas Aguilera, Universidad de Guadalajara, 2006-2007
Fast 3D/2D Region Growing (MEX) by Christian Wuerslin, Stanford University, 2013-2015.
Fiji Connect is using MIJ, a Java package for bi-directional communication and data exchange from Matlab to ImageJ/Fiji, developed by Daniel Sage, Dimiter Prodanov, Jean-Yves Tinevez and Johannes Schindelin, 2012. MIJ is not supplied with Microscopy Image Browser and should be installed using Fiji
FINDJOBJ - find java handles of Matlab graphic objects by Yair Altman, 2007-2013
FRANGI filter by Marc Schrijver and Dirk-Jan Kroon, University of Twente 2001-2009
Image Edge Enhancing Coherence Filter by Dirk-Jan Kroon & Pascal Getreuer, University of Twente, 2009
IMCLIPBOARD function by Jiro Doke, MathWorks, 2010 is used in the snapshot tool and import from system clipboard
IceImarisConnector written by Aaron C. Ponti, ETH Zurich is used for connection to Imaris
Image Measurement Utility written by Jan Neggers, Eindhoven Univeristy of Technology was used as a basis for the Measure Tool and re-written roiRegion class.
IMGAUSSIAN by Dirk-Jan Kroon, University of Twente, implementation 2009 is used in the 3D Gaussian filter
Local normalization by Guanglei Xiong at Tsinghua University, Beijing, China, 2005
MATTOMO is a part of PEET (Particle Estimation for Electron Tomography) package, developed at Boulder Laboratory for 3-D Electron Microscopy of Cells was used for export of models to IMOD format
MAXFLOW/MINCUT algorithm, v.2.22 written by Yuri Boykov, University of Western Ontario and Vladimir Kolmogorov, Microsoft research, Cambridge.
MAXFLOW/MINCUT Matlab wrapper is written by Michael Rubinstein, Google
NRRD, Nearly Raw Raster Data format is implemented using Projects:MATLABSlicerExampleModule written by John Melonakos for NRRD reading using TEEM; and a custom function for reading metadata based on NRRD Format File Reader written by Jeff Mather, 2012
OMERO Matlab bindings (should be downloaded separetly) are used for connection to OMERO servers
P_JSON, highly portable JSON parser function is written by Nedialko, 2009
Random Forest Classifier is based on Verena Kaynig implementation with utilization of randomforest-matlab by Abhishek Jaiantilal
Region Adjacency Graph (RAG) function is written by David Legland, INRA, France, 2013
REGIONPROPS3 function is written by Chaoyuan Yeh, University of Southern California, 2014
RENDERTEXT function by Davide Di Gloria, Universita di Genova, 2010 is utilized for addition of text to image
Rendering with Fiji is based on Hardware accelerated 3D viewer for MATLAB written by Jean-Yves Tinevez, Institut Pasteur, 2011
Rendering with Matlab is using VIEW3D function written by Torsten Vogel, 1999
SLIC (Simple Linear Iterative Clustering) written by Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Süsstrunk, Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland, 2015 was utilized for the superpixels mode of the Brush tool and for the Graphcut segmentation.
STLWRITE by Sven Holcombe, University of Michigan 2008-2015 for saving models using the STL format
VIEWER3D by Dirk-Jan Kroon, Focal Machine Vision en Optical Systems was used as a basis for the volume rendering of datasets
XLSWRITE mod by Barry Dillon, AON Insurance Brokers 2010
XML2STRUCT and STRUCT2XML by Wouter Falkena, Delft University of Technology, 2010

Color palettes are generated with help of

Fast/Robust Template Matching (2009-2011) by Dirk-Jan Kroon, University of Twente was used for alignment of datasets in MIB version 1.22 and earlier

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