display

Visualization of data, documents
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 07/10/13
  • Minor correction: 07/10/13

ImagineMVS : 3D reconstruction in multiple view stereovision

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 20101112 - 12/11/2010
  • License(s): Proprietary licence
  • Status: internal use
  • Support: maintained, no ongoing development
  • Designer(s): Renaud Keriven
  • Contact designer(s): renaud.keriven @ acute3D.com
  • Laboratory, service: Acute3D company

 

General software features

A complete algorithmic pipeline for reconstruction of a 3D model from photographs.

The software takes as input calibrated views (that is, photographs with camera posed and oriented in space and internal parameters known). As output, it yields a textured 3D mesh. The steps are the following:

  • estimation of dense correspondences between images by plane sweeping,
  • triangulation to get a point cloud,
  • tetrahedral meshing of the point cloud and removal of hidden faces to get an initial mesh,
  • mesh optimization by incremental minimization of an energy balancing data fidelity and regularity,
  • creation from view fragments of a texture atlas to apply to the mesh.
Context in which the software is used

Internal use in IMAGINE project (École des Ponts ParisTech/CSTB).

This software is at the core of the start-up Acute3D.

Publications related to the software

Vu Hoang Hiep, Renaud Keriven, Patrick Labatut and Jean-Philippe Pons. Towards high-resolution large-scale multi-view stereo, Proceedings of CVPR 2009, pp. 1430-1437.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 22/09/13
  • Minor correction: 22/09/13

Imagine++ : C++ libraries for teaching, image processing and numerical computation

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 4.0.1 - Septembre 2012
  • License(s): not yet chosen
  • Status: stable release, under development
  • Support: maintained, ongoing development
  • Designer(s): R. Keriven, P. Monasse
  • Contact designer(s): monasse @ imagine.enpc.fr
  • Laboratory, service:

 

General software features

4 libraries are proposed:

  • Common: multi-dimensional arrays with shared memory for fast copy, static size vector and matrices.
  • LinAlg: linear algebra with dynamic size vectors and matrices, solution of linear systems, matrix decompositions (SVD, QR, Cholesky).
  • Graphics: windows with tabs, 2D graphics (elementary shapes, bitmaps) and 3D graphics (elementary volumes, triangulated meshes), animations, mouse and keyboard events.
  • Images: input/output in standard formats, geometric transformations, interpolation, standard filters.
Context in which the software is used

The focus is put on easy usage and efficiency. Display relies on Qt and OpenGL, linear algebra on Eigen.

  • Teaching programming: allows writing easily recreational software, with protection from classical errors that are critical for performance by using shallow copy for images and matrices.
  • Research in image processing and computer vision: additional modules for optimization, multi-view geometry and interest point dectection are used internally.
Publications related to the software
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 19/09/13
  • Minor correction: 19/09/13
  • Index card author: Eric Hivon (IAP)
  • Theme leader : Dirk Hoffmann (Centre de Physique des Particules de Marseille (CPPM-IN2P3))

HEALPix : data analysis, simulation and visualisation on the sphere

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 3.11 - April 2013
  • License(s): GPL - GPLv2
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Eric Hivon; Martin Reinecke; Krzysztof M. Gorski; Anthony J. Banday; Benjamin D. Wandelt; Emmanuel Joliet; William O'Mullane; Cyrille Rosset; Andrea Zonca
  • Contact designer(s): hivon at iap.fr
  • Laboratory, service: MPA (Garching, Allemagne), Caltech (Pasadena, CA,Etats-Unis), TAC (Copenhague, Danemark), ESAC (Madrid, Espagne), JPL (Pasadena, CA, Etats-Unis), ESO (Garching, Allemagne)

 

General software features

The HEALPix software implements the HEALPix (Hierarchical Equal Area iso-Latitude Pixelation) pixelation of the sphere. Initially developed for the simulation and analysis of ESA Planck satellite observations (dedicated to the study of the Cosmic Microwave Background (CMB) anisotropies, whose first results were delivered in March 2013), this software and its pixelation algorithm have become standard tools in the simulation and analysis of data on the sphere, including the NASA WMAP satellite, also dedicated to CMB observation, and the Pierre Auger ground based observatory for high energy cosmic rays, and are used for other astrophysical and geological studies.

Main features of the pixelation

At a given resolution, all HEALPix pixels have the same surface area, even if their shape varies slightly. Thanks to the hierarchical feature of the pixelation, upgrading its resolution to the next level simply amounts to divide each pixel into four sub-pixel of the same area. This allows quick and efficient upgrading and downgrading operations of existing maps.

Since the pixels are regularly spaced on iso-latitude rings, Spherical Harmonics can be computed very efficiently. The synthesis or analysis up to multipole Lmax  of a spherical data set containing Npix pixels is reduced from    Npix Lmax2   to   Npix½ Lmax2  compared to non iso-latitude pixelation.

Features of the software package

The represents data on the sphere, and enables analysis or simulation of these maps in (scalar or spin-weighted) Spherical Harmonics, as well as various kinds of statistical analyses and processing. Portable FITS files are used for input and output. The list of available functions includes:

  • generation of random maps (gaussian or not) from an arbitrary angular power spectrum,
  • computation of the angular power spectrum (or angular correlation function) of a map,
  • convolution of a spherical map with an arbitrary circular window,
  • tessellation of the sphere and pixel processing supported down to a pixel size of 0.4 milliarcseconds (equivalent to 3.5 1018 pixels on the sphere),
  • median filtering of a map,
  • search of local extrema in a map,
  • query of pixels located in user defined disks, triangles, polygons, ...
  • processing of binary masks to identify 'holes' in order to fill them, or to apodize masks,
  • visualization of HEALPix sky maps either on the whole sky (using Mollweide or orthographic projections) or on a patch (gnomic or cartesian projections),
  • output in Google Map/Google Sky and DomeMaster format.

The most expensive operations, such a Spherical Harmonics Transform have been carefully optimised and benefit from a shared memory parallelisation based on OpenMP.

Contents of the software package

The software is available in C, C++, Fortran90, IDL/GDL, Java and python. The following modules are provided in each of these languages:

  • a library of tools (subroutines, functions, procedures, modules, classes, ...depending on languages) covering most of the functionnalities described above, as well as supporting ancillary tools (eg, parameter file parsing),
  • a set of stand-alone facilities based on the library above and each implementing one of HEALPix major features (map generation or analysis, filtering, resolution udgrade or downgrade, visualization). These applications are generally run via an interactive dialog or an ASCII parameter file. Their source code can be used as a starting point for user specific developments,
  • an extensive PDF and/or HTML documentation describing in details the API, inner working and limitations of each tool and application.

Finally, some tools (interactive script and Makefile) are provided to manage and facilitate the compilation and installation of one or several of the libraries and facilities, for most combinations of hardwares, operating systems, compilers, ...

Third Party Developements

One can distinguish two kinds of third party developements (defined as not (yet) being part of the official HEALPix package described above):

  • new functionalities, for instance many tools based on Minkowski functionals, wavelets (iSAP, MRS, S2LET, SphereLab), or structure identification (DisPerSE) developed by various research teams can be applied to data stored in HEALPix format,
  • translations, re-implementations or wrapping of (some of) existing functionalities, for instance in Matlab/Octave (Mealpix) and Yorick (YHeal) are available. (See (almost) exhaustive list.)

Context in which the software is used

Software used for the analysis of Planck satellite data.
Data format supported by Aladin visualisation software to represent diffuse astronomical data on the sky.

Publications related to the software

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 11/09/13
  • Minor correction: 11/09/13

TreeCloud : building tree cloud visualizations from texts

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.3 - 13/12/2009
  • License(s): GPL
  • Status: under development
  • Support: maintained, ongoing development
  • Designer(s): Philippe Gambette ; Jean VĂ©ronis
  • Contact designer(s):

    P. Gambette

  • Laboratory, service:

 

General software features

TreeCloud generates a tree cloud from a text, that is a word cloud whose words are arranged around a tree which reflects their semantic proximity inside the text.

Context in which the software is used

The main application of the tree clouds built by TreeCloud is to provide a quick overview of the content of a text. It is also possible to use them for a deeper analysis of the texts, included in a textometric approach (text analysis using software tools and statistical methods). Then, the tree cloud will help the user to fomalize some hypotheses, or test them. It can therefore lead to use other textometric tools to confirm these hypotheses, or to visualize the results of the output of those tools.

Publications related to the software

Philippe Gambette and Jean VĂ©ronis: Visualising a Text with a Tree Cloud, In Locarek-Junge H. and Weihs C., editors, Classification as a Tool of Research, Proc. of IFCS'09 (11th Conference of the International Federation of Classification Societies) Studies in Classification, Data Analysis, and Knowledge Organization 40, p. 561-570, 2010.

Delphine Amstutz and Philippe Gambette (in French): Utilisation de la visualisation en nuage arboré pour l'analyse littéraire, Statistical Analysis of Textual Data (Proc. of JADT'10), p. 227-238, 2010.

Philippe Gambette, Nuria Gala and Alexis Nasr(in French): Longueur de branches et arbres de mots, Corpus 11, p. 129-146, 2012.

William Martinez and Philippe Gambette (in French): L'affaire du Médiator au prisme de la textométrie, Texto !, to appear, 2013.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/04/13
  • Minor correction: 18/04/13

PST-Cox : PSTricks library for drawing 2D-projections of regular complex polytopes

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0 - fĂ©vrier 2008
  • License(s): LGPL
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): Jean-Gabriel Luque
  • Contact designer(s): Jean-Gabriel.Luque@univ-mlv.fr
  • Laboratory, service:

 

General software features

PST-Cox is a library of LaTeX macros allowing to draw 2D-projections of regular complex polytopes. Regular complex polytopes are hyperplane arrangements satisfying certain constraints, and whose automorphism graphs are generated by pseudo-reflections (complex reflections). These objects generalize the classical Platonic solids.

Context in which the software is used

This software is used to illustrate research results (see references).

Publications related to the software
  • Briand, J.-G. Luque, J.-Y. Thibon, and F. Verstraete. The moduli space of three qutrit states. Journal of Mathematical Physics. Vol. 45. 2004. pp. 4855-4867.
  • J.-G. Luque. Invariants des hypermatrices. Habilitation Ă  diriger des recherches. I.G.M., UniversitĂ© de Marne-la-VallĂ©e. 2007.
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/04/13
  • Minor correction: 12/09/13

Euclidean skeletons : methods for robust Euclidean skeletonization in 2D and 3D

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0 - sept. 2010
  • License(s): CeCILL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Michel Couprie
  • Contact designer(s): coupriem @ esiee.fr
  • Laboratory, service:

 

General software features

Skeletons suffer from the lack of stability with respect to noise. This is why, in real applications, skeleton filtering is a
crucial issue. This software implements recently introduced methods for obtaining robust, filtered Euclidean skeletons in 2D and 3D discrete spaces.

Context in which the software is used

This software has been built for finding and validating the results of the related publications.

Publications related to the software

[CCT10] J. Chaussard, M. Couprie and H. Talbot: "Robust skeletonization using the discrete lambda-medial axis", Pattern Recognition Letters, Volume 32, Issue 9, 1 July 2011, Pages 1384–1394.

[SCL09] A. Vital SaĂşde, M. Couprie and R. Lotufo: "Discrete 2D and 3D Euclidean medial axis in higher resolution", Image and Vision Computing, Vol. 27, pp. 354--363, 2009.

[CCZ07] M. Couprie, D. Coeurjolly and R. Zrour: "Discrete bisector function and Euclidean skeleton in 2D and 3D", Image and Vision Computing, Vol. 25, pp. 1543-1556, 2007.

Other publications: http://www.esiee.fr/~coupriem/es/ES_biblio.html

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 09/01/13
  • Minor correction: 12/09/13

Topological smoothing : method for smoothing 2D and 3D objects

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0 - 2004
  • License(s): CeCILL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Michel Couprie
  • Contact designer(s): coupriem @ esiee.fr
  • Laboratory, service:

 

General software features

This software implements a method for smoothing 2D and 3D objects in binary images while preserving topology. Here, objects are defined as sets of grid points, and topology preservation is ensured by the exclusive use of homotopic transformations defined in the framework of digital topology. Smoothness is obtained by the use of morphological openings and closings by metric discs or balls of increasing radius, in the manner of alternating sequential filters from the field of mathematical morphology.

Context in which the software is used

This software has been built for finding and validating the results of the paper [CB04].

Publications related to the software

[CB04] Michel Couprie, G. Bertrand: "Topology preserving alternating sequential filter for smoothing 2D and 3D objects", Journal of Electronic Imaging, Vol. 13, No. 4, pp. 720-730, 2004.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/07/12
  • Minor correction: 28/05/14

Morse : Generic simulator for robotics

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.2 - january 2014
  • License(s): BSD
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Main developers: Arnaud Degroote (LAAS-CNRS), Gilberto Echeverria (LAAS-CNRS), Michael Karg (TUM), SĂ©verin Lemaignan (LAAS-CNRS). See the full list.
  • Contact designer(s): morse-dev AT laas DOT fr
  • Laboratory, service: Technische Universität MĂĽnchen (TUM) full list

 

General software features

MORSE is a generic simulator for academic robotics. It focuses on realistic simulation of small to large environments, indoor or outdoor, with one to over a dozen of autonomous robots. It provides a set of standard sensors (cameras, laser scanner, GPS, odometry,...), actuators (speed controllers, high-level waypoints controllers, generic joint controllers) and robotic bases (ATRV, generic 4 wheel vehicle, PR2,...) used in robotics research laboratories. New components can easily be added.

Morse can use and test software components interacting through several middlewares used in robotics, including: Fiche Plume pocolibs, yarp and ROS.

One of the main design choice for MORSE is the ability to control the degree of realism of the simulation, form photo-realistic rendering for image processing to semantic levels, avoiding heavy processing to extract information.

Morse is based on the Fiche Plume Blender modelling and real-time 3D rendering environment and on the Bullet physics simulator engine.

Context in which the software is used

Academic research in robotics, development and debugging of software components, teaching,...

Publications related to the software
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 16/11/11
  • Minor correction: 16/11/11

NemoFish : three-dimensional fluorescence in situ hybridization (3D-FISH)

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.5 - 2009/12/07
  • License(s): Other - Creatice Commons V2 (freeware, not open source)
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Eddie Iannuccelli, Thomas Boudier
  • Contact designer(s): eddie.iannuccelli@toulouse.inra.fr
  • Laboratory, service:

 

General software features

Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories.

Context in which the software is used

Three-dimensional fluorescence in situ hybridization (3D-FISH)

Publications related to the software

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
E. Iannuccelli; F. Mompart; J. Gellin; Y. Lahbib-Mansais; M. Yerle; T. Boudier
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq013

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 02/05/11
  • Minor correction: 02/05/11

TASE : online tool for searching candidate regions from SNPs data

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 5.0 - 11/01/2011
  • Status: internal use
  • Support: maintained, ongoing development
  • Designer(s): M.HEBRARD, C.HAMEL, G.MANES, I.MOUGENOT
  • Contact designer(s): maxime.hebrard@inserm.fr
  • Laboratory, service:

 

General software features

TASE is a webtool dedicated to the study of hereditary diseases.

  • From a whole-genome SNP scan (Single Nucleotide Polymorphism), the soft identifying candidate regions which could contain the gene causing the disease.
  • TASE analyze data of DNA chips from 10K to 900K.
  • TASE have a web interface and is easy to use.

language: Javascript and Perl-cgi.

Other functions :

  • Display family tree using cranefoot (French cranefoot card).
  • Specific tests according family profile : autosomal dominante or recessive transmission, consanguineous family or not.
  • Select whitch individual you want to test and his status (sick or healthy).
  • Display graphic results in whole genome view or chromosome specific.
Context in which the software is used

Our team study hereditary retinal distrophies that are monogenic and very heterogeneous diseases.
TASE analyzes whole genome data (SNP chips) and display candidate regions.
Then these regions are sequencing to identify causative mutation.

Exemple of use :

  • Autosomal dominante transmission:
    • Identifying causative gene among known genes.
    • Finding unknown gene or locus in large family.
  • Autosomal recessive transmission:
  • Identifying causative gene among known genes, even small family (only 3 individuals).

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