Acknowledgements

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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

Special thanks come to

Radhakrishna Achanta, Ecole Polytechnique Federale de Lausanne (EPFL) for the mex code for SLIC supervoxels and superpixels
Tom Boissonnet (EMBL) and Elena Bertseva (University of Copenhagen) for extensive testing
John Heumann, The Boulder Laboratory For 3-D Electron Microscopy of Cells for help with Mattomo
Konstantin Kogan, University of Helsinki for assistance with Mac OS
David Legland, INRA, France for modification of the Region Adjacency Graph (imRAG) function for detection of indices between watershed regions and help with few other functions
Vladimir Moltchanov, for discussions on software architectures
Henrik P Sahlin Pettersen, Norwegian University of Science and Technology/St. Olavs hospital, Trondheim for driving DeepMIB for pathology

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
API documentation of classes was done using MTOC++ - Doxygen filter for MATLAB and tools written by Martin Drohmann (Universitat Munster) and Daniel Wirtz (Universitat 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 is used for anisotropic diffusion filtering of images
BIO-FORMATS by Melissa Linkert, Curtis Rueden et al. 2002-2013 is utilized for reading of proprietary microscopy image formats using the codeBio</code> checkbox
BMxD external filters by Kostadin Dabov et al., Tampere University of Technology, Finland 2007-2014 can be used with MIB, when separately installed on the system to filter the images
BWDISTSC for 3D Euclidean distance transform for variable data aspect ratio written by Yuriy Mishchenko (Toros University, 2007-2013) is used for separation of anisotropic objects in 3D and calculation of distance maps
Custom GINPUT, written by Jiro Doke (MathWorks 2016) to get coordinates of a clicked point
CELL MIGRATION IN SCRATCH WOUND ASSAYS by Constantino Carlos Reyes-Aldasoro, City, University of London was used for the wound healing assay tool
DnD_uifigure: drag & drop functionality for AppDesigner components written by Xiangrui Li (the Ohio State University, 2020-2023)
Drag & Drop functionality for JAVA GUI components written by Maarten van der Seijs (Delft University of Technology, the Netherlands, 2015)
DRAWREGIONBOUNDARIES a function to draw boundaries of labeled regions in an image when working with brush, 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 mibCalcShifts.m
Elastic Distortion filter is based on Elastic Distortion Transformation on an image by David Franco (Catholic University of Parana)
EXPORT_FIG function to add measurements to snapshots is written by Oliver Woodford and Yair Altman
Fast 3D/2D Region Growing (MEX) by Christian Wuerslin (Stanford University, 2013-2015) is used for the region growing tool
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
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)
FSTACK extended depth-of-field image from focus sequence using noise-robust selective all-in-focus algorithm by Said Pertuz (Universitat Rovira i Virgili, Tarragona, Spain 2013) is used in the intensity projection tool
HistThresh toolbox by Antti Niemistö (Tampere University of Technology, Finland) is used for most of the global histogram-based thresholding methods
Image Edge Enhancing Coherence Filter Dirk-Jan Kroon, Pascal Getreuer (University of Twente)
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) is used as a basis for the Measure Tool and re-written roiRegion class
IMCLIPBOARD function by Jiro Doke, MathWorks, 2010 is used in the snapshot tool and import from system clipboard
IMGAUSSIAN by Dirk-Jan Kroon (University of Twente), implementation 2009 is used in the 3D Gaussian filter
MATGEOM, a MATLAB geometry toolbox for 2D/3D geometric computing is written David Legland (INRA, France, 2013) is used in some functions
MATTOMO is a part of PEET (Particle Estimation for Electron Tomography) package, developed at Boulder Laboratory for 3-D Electron Microscopy of Cells is 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) is used in the Graphcut tool
MAXFLOW/MINCUT MATLAB wrapper is written by Michael Rubinstein (Google) is used in the Graphcut tool
NUM2CLIP function by Grigor Browning, 2005 is used to copy column items to the system clipboard
NRRD, Nearly Raw Raster Data format is implemented using Projects:MATLABSlicerExampleModule written by John Melonakos for NRRD reading using http://teem.sourceforge.net/TEEM; and a custom function for reading metadata based on NRRD Format File Reader written by Jeff Mather, 2012
NRRD NHDR reader and writer functions by Gaetan Rensonnet, 2018 is used to read NRRD format files on MacOS
OMERO MATLAB bindings (included into the compiled version, but should be downloaded separetly for the MATLAB version) are used for connection to OMERO servers
P_JSON, highly portable JSON parser function is written by Nedialko, 2009 is used for work woth HDF5 files
PATCHNORMALS by Dirk-Jan Kroon (University of Twente) implementation 2009 is used for calculation of normals during export of surfaces to Imaris
POOLWAITBAR class is based on the code submitted by Edric Ellis
Prettify MATLAB html by Harry Dymond, University of Bristol was used to prettify MIB documentation
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) is used in the Graphcut tool
REGIONPROPS3 function is written by Chaoyuan Yeh (University of Southern California, 2014) is used for quantitation some object properties in 3D
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
SAM segmentation is using networks and code from Segment-anything written by 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, 2023
SAM segmentation is using networks and code from Segment-anything for Microscopy written by Archit A, Nair S, Khalid N, Hilt P, Rajashekar V, Freitag M, Gupta S, Dengel A, Ahmed S, Pape C, 2023
SLIC (Simple Linear Iterative Clustering) written by Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine S?sstrunk, 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
UIGETFILE_N_DIR by Tiago / Peugas is used for selection of multiple directories
VIEWER3D by Dirk-Jan Kroon (Focal Machine Vision en Optical Systems) is used as a basis for the volume rendering of datasets
Violin plot by Holger Hoffmann, 2015 used for visualization of results in some analysis functions
XLWRITE: Generate XLS(X) files without Excel on Mac/Linux/Win by Alec de Zegher (NV Bekaert SA 2013)
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

ICONS AND IMAGES

Some icons used in MIB were provided by Icons8.com (<https://icons8.com https://icons8.com>), license information
Some images were generated using stable-diffusion image generative AI

OLDER SCRIPTS

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 (used in MIB 0.x and 1.x).
EXTREMA functions by Carlos Adrian Vargas Aguilera, Universidad de Guadalajara, 2006-2007 (used in MIB 0.x and 1.x)
Fast/Robust Template Matching (2009-2011) by Dirk-Jan Kroon, University of Twente was used for alignment of datasets (used in MIB 0.x and 1.x-1.22). Image Edge Enhancing Coherence Filter> by Dirk-Jan Kroon & Pascal Getreuer, University of Twente, 2009 (used in MIB 0.x and 1.x).
Local normalization by Guanglei Xiong at Tsinghua University, Beijing, China, 2005 (used in MIB 0.x and 1.x).

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