This project would not have been possible without all the open source projects and code I relied on and the inspiration from ADMCF IRB Barcelona facility users projects, including the sample images that they kindly shared with me. I also thank all my colleagues for their support, kindness, and all people who have seen and heard me hallucinating about LOBSTER over the past years!
Sébastien Tosi
Third Party software
I would like to thank the autors of these MATLAB File Exchange contributions and open source projects:
- Graph analysis toolbox, Leo Grady (GNU general public license) http://leogrady.net/software/
- Basic Image Features (BIFs) implementation, L. D. Griffin et al. https://github.com/GriffinLab/BIFs
- Isthmus thinning 3D (Palagyi 2014), code adapted from ibcenterline.c provided by K. Palagyi
- Local Binary Pattern, Ahonen http://www.cse.oulu.fi/CMV/Downloads/LBPMatlab
- Local Phase Quantization Ojansivu V & Heikkilä J (2008) Blur insensitive texture classification using local phase quantization. Proc. Image and Signal Processing (ICISP 2008), 5099:236-243. http://www.cse.oulu.fi/CMV/Downloads/LPQMatlab
- Image and video denoising by sparse 3D transform-domain collaborative filtering, BM3D, Kostadin Dabov (specific open source license, see url) http://www.cs.tut.fi/~foi/GCF-BM3D/
- CellProfiler Propagate 2D method (updated to support 3D images), Anne Carpenter (BSD 3-Clause License) https://github.com/CellProfiler/CellProfiler
- Preconditioning of phase contrast image Zhaozheng Yin, Hang Su, Zhaozheng Yin, Takeo Kanade, Seungil Huh Phase Contrast Image Restoration via Dictionary Representation of Diffraction Patterns. The 15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2012: 615-622 https://www.albany.edu/celltracking/
- Stain normalization, Mitko Veta Macenko, M. et al. A method for normalizing histology slides for quantitative analysis. ISBI 9, 1107–1110 (2009), from Matlab Central (specific open source license, see license in folder or at URL) https://github.com/mitkovetta/staining-normalization
- Bresenham line 3D from Tools for NIfTI and ANALYZE image, Jimmy Shen, adapted from B.Pendleton. line3d - 3D Bresenham's (a 3D line drawing algorithm) https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
- Hessian based Frangi Vesselness filter, Dirk-Jan Kroon https://www.mathworks.com/matlabcentral/fileexchange/24409-hessian-based-frangi-vesselness-filter?focused=5148984&tab=function
- Jerman Enhancement Filter, Tim Jerman, Dirk-Jan Kroon https://www.mathworks.com/matlabcentral/fileexchange/63171-jerman-enhancement-filter
- interparc (function renamed to arclength), John D'Errico https://www.mathworks.com/matlabcentral/fileexchange/34874-interparc
- 3D rendered adapted from OpenGL .NET Examples, Dirk-Jan Kroon https://it.mathworks.com/matlabcentral/fileexchange/23792-opengl-net-examples
- imtool3D, Justin Solomon, code modified to support colour annotation masks. https://www.mathworks.com/matlabcentral/fileexchange/40753-imtool3d
- PIV suite, Jiri Vejrazka (specific open source license, see code folder) https://www.mathworks.com/matlabcentral/fileexchange/45028-pivsuite
- Accurate Fast Marching, Dirk-Jan Kroon (specific open source license, see code folder) https://fr.mathworks.com/matlabcentral/fileexchange/24531-accurate-fast-marching
- Skel2Graph, Philip Kollmannsberger https://www.mathworks.com/matlabcentral/fileexchange/43527-skel2graph-3d
- Beautiful and distinguishable line colors + colormap, Jonathan C. Lansey (specific open source license, see url) https://www.mathworks.com/matlabcentral/fileexchange/42673-beautiful-and-distinguishable-line-colors-colormap?focused=b7ba50c5-8fd6-2d2e-144b-8ffb2b2db013&tab=function
- RegularizeData3D, John D'Errico https://www.mathworks.com/matlabcentral/fileexchange/46223-regularizedata3d
- STL writer, Sven Holcombe (specific open source license, see url) https://www.mathworks.com/matlabcentral/fileexchange/20922-stlwrite-write-ascii-or-binary-stl-files
- 3D structuring element, Jan Simon https://www.mathworks.com/matlabcentral/fileexchange/47937-3d-structuring-element-sphere
- textprogressbar, Paul Proteus (specific open source license, see url) https://www.mathworks.com/matlabcentral/fileexchange/28067-text-progress-bar
- Fast Non-local mean image denoising implementation, Yue Wu https://www.mathworks.com/matlabcentral/fileexchange/38200-fast-non-local-mean-image-denoising-implementation
- Extended depth of field, Said Pertuz https://de.mathworks.com/matlabcentral/fileexchange/55115-extended-depth-of-field?focused=5906461&tab=function
- Minimum volume enclosing ellipsoid, Nima Moshtagh https://www.mathworks.com/matlabcentral/fileexchange/9542-minimum-volume-enclosing-ellipsoid?s_tid=prof_contriblnk
- Load/save GUI state, sco1 (GitHub user) https://github.com/StackOverflowMATLABchat/GUIstate