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VOXELO : a project for computing and visualizing geometric-topological features for nD digital images. Pedro Real Jean-Luc Mari. CATIMAG ’08, Seville. University of Marseille 2 LSIS Laboratory “Image & Models” Team France. University of Seville Dept. Matematica Aplicada I Spain.
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VOXELO:a project for computing and visualizinggeometric-topological features for nD digital images Pedro Real Jean-Luc Mari CATIMAG ’08, Seville University of Marseille 2LSIS Laboratory“Image & Models” TeamFrance University of SevilleDept. Matematica Aplicada ISpain
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Example of discrete virtual world
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Example of discrete virtual world
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Example of discrete virtual world
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia • A software to run and test AT algorithms • Implementation of algebraic-topological methods (originally in 14-adjacency)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia • A software to run and test AT algorithms • Implementation of algebraic-topological methods (originally in 14-adjacency) First of all: conversion from voxels to simplicial complex
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia • A software to run and test AT algorithms • Implementation of algebraic-topological methods (originally in 14-adjacency) First of all: conversion from voxels to simplicial complex
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville What is Voxelo? • Initially, a pedagogical tool • To handle and analyze discrete worlds (virtual LEGO) in primary schools • Supported by Spanish Ministry of Science and Technology and Consejería de Innovación of Junta de Andalucia • A software to run and test AT algorithms • Implementation of algebraic-topological methods (originally in 14-adjacency)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • Moka • Univ. Poitiers, France • 3D modeler based ontopology http://www.sic.sp2mi.univ-poitiers.fr/moka
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • CHomP • Computational Homology Project • Software + library http://chomp.rutgers.edu
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • Voxel3D • Voxel based 3D modeling software • Designed for “3D beginners” • Easy to use • No topologicalfeatures http://www.everygraph.com (Shareware)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • QVox • Volumetric data visualizer and editor • Edition of voxels or surfels • Homotopic thinning algorithms using (6,18), (6,26), (18,6) and (26,6) pairs • Re-sampling, binarization, inversion, mirrors, crop, merge volumes, fill cavities… • OBJ export • Created by Sébastien Fourey (GREYC, Caen, France) • http://qvox.sourceforge.net
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • QVox • Snapshots
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • QVox • Snapshots
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • VolumeGraphics Studio • “Solutions about voxels” • http://www.volumegraphics.com • Visualization software • Raytracer rendering • Slices exploration • DICOM viewer • Geometry analysis • Commercial software
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Similar softwares • Other softwares… • Coma • Univ. Vienna, Austria
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • The need of a framework where everybody can contribute • All the code is about to be moved on a SVN repository • Subversion (SVN) is an open source version control system (previously CVS) • Commonly used in software development in order to manage source code • Adapted to a team of developers
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Multiplatform software • Currently only a Windows software… • Porting the Windows API to Qt • ( Master students work mostly under Linux ) • To keep: • C++ language • OpenGL
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Modularity • Each Master student involved in the project has to be able to add features easily CSG voxel tools VOXELO kernel Morphomath Topological analysis toolkit Thinning module
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Integration of 26-adjacency • Work in progress
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Integration of 26-adjacency • Work in progress • Implementation of CSG operations on digital volumes • Integration of morphological operations
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Implementation of a thinning module • Homotopic thinning using simple points • Directly in the homology computation
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Handling of nD digital images • Topology analysis over 4D, etc… • Understanding of topological changes over time
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Handling of nD digital images • nD morphological operators (Segmentation of heart data in 4D)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Improvements • Enhancement to get “good” (geometrically speaking) representative cycles for the homology and cohomology generators • To deal with other representation formalisms for digital volumes (octrees, functional representations…)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Overview • What is Voxelo? • Similar softwares • Improvements and expectations(“TO DO” list) • Who’s involved? How to contribute?
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Who’s involved • Pedro Real (Univ. Seville) • Rocio Gonzalez-Diaz (Univ. Seville) • Javier Sanchez-Pelaez (Univ. Seville) • Former developer • Jean-Luc Mari (Univ. Marseille) • Helena Molina-Abril (Univ. Seville) • Nicolas Jesson (Univ. Marseille, Master student) • Features related to simplicial complexes in 26-adjacency • Simplicialization of octrees • José-Manuel Mercado-Martinez (Univ. Seville + Erasmus student currently in Marseille) • Linux port
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville How to contribute • Declaration of intent • The will to design of a tool for discrete geometry and topological analysis • A platform to run and test algorithms • A way for students to quickly have a feedback on their projects • Without reinventing the wheel…
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville How to contribute • Send me an email mari@univmed.fr • Create an account (Voxelo SVN repository) • Integrate sample code to Voxelo • Implantation of specific algorithm within Voxelo platform • Take time to consider how to integrate specific features • Everybody is welcome :)
P. Real and J.-L. Mari - VOXELO: a project for computing geometric-topological features - CATIMAG ’08, Seville Thank you for your attention