UNIX-like

Software (mostly Free Libre Open Source Software - FLOSS) that runs on Unix-derived systems such as Linux
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 19/11/13
  • Minor correction: 19/11/13

ScientiFig : create publication-ready scientific figures

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: 2.6 - 02/10/2013
  • License(s): BSD -
    ScientiFig uses the Apache BATIK and XML-apis libraries as well as the BSD Rsession library.
  • Status: beta release
  • Support: maintained, no ongoing development
  • Designer(s): Benoit Aigouy
  • Contact designer(s): Benoit Aigouy
  • Laboratory, service:

 

General software features

Scientists often build figures for publications and talks. To create these figures, they usually rely on powerful tools that are designed for graphic designers to produce artistic figures and are therefore only poorly suited to build scientific figures.

We here present an ImageJ/FIJI plugin called ScientiFig that is devoted to the building of research figures. Our tool can assemble and maintain complex panels containing images with different aspect ratios and associate scalebars, text annotations and ROIs to these panels. Interestingly, our software will always preserve the position of these associated elements even when figure size changes. ScientiFig can export figures as png with a transparent background for a better integration in office documents and as vector graphics that can be finalized using a vector graphics editor. Last but not least, ScientiFig can format figures for various scientific reviews and for example offer to substitute fonts or to resize the figure to better match the journal guidelines (if a journal style does not exist, it can be created using the embedded editor).

For comparison, please find below two alternative tools:

Context in which the software is used

ScientiFig is a tool to buid and format images for scientific publications.

Publications related to the software

ScientiFig: a tool to build publication-ready scientific figures. Aigouy B, Mirouse V. Nat Methods. 2013 Oct 30;10(11):1048. doi: 10.1038/nmeth.2692.

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
  • Index card author: Luc Hogie (I3S)
  • Theme leader : Dirk Hoffmann (Centre de Physique des Particules de Marseille (CPPM-IN2P3))

jaseto : JAva SErialisation TOolkit

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: 2013.08.30.14.13.40 - 2013.08.30
  • License(s): LGPL
  • Support: maintained, ongoing development
  • Designer(s): Luc Hogie
  • Contact designer(s): luc.hogie@cnrs.fr
  • Laboratory, service:

 

General software features

Jaseto is a Java library enabling the description of Java objects in XML, and conversely, the creation of Java object from their XML description. This process is commonly referred to as (de)serialization or (un)marshalling. It is usually employed to make the data persistent across executions, by storing the XML text on disk or into XML databases.

Other libraries such as XStream, Castor, and JAXB are other viable solutions. Compared to these, Jaseto offers a cleaner and shorter source code, better performance (its proves 10× faster than Castor and XStream), a solution to some of their limitations: no need to know in advance the type of an object to be deserialized, no need to resort to annotations, no need to follow the JavaBean spec, etc.

Context in which the software is used

Jaseto is used in our lab in order to store and export graph and configuration data.

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: 07/10/13
  • Minor correction: 07/10/13

OpenMEEG : resolution of forward problems in electroencephalography and magnetoencephalography

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: 2.1 - 17/08/2011
  • License(s): CeCILL-B
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Theodore Papadopoulo
  • Contact designer(s): Theodore.Papadopoulo @ inria.fr
  • Laboratory, service:

 

General software features

OpenMEEG, now developed by the Athena project (INRIA Sophia Antipolis), is dedicated essentially to the resolution of the forward MEG (magneto-encephalography) and EEG (electroencephalography) problems. For this purpose, it uses a finite surface element method (BEM) that involves at the same time surface potentials and normal currents, which yields symmetrical matrices unlike classical approaches. This approach yields more precise results as well.

Though developed essentially for problems related to brain, OpenMEEG can also be used in other contexts such as electrocardiography, nerve simulation or electrical propagation in the cochlea.

OpenMEEG starts from a geometric-physical description of the head as nested surfaces in the form of meshes (interfaces between head tissues) and of conductivities of the surface delimited tissues. Then, with a description of EEG and/or MEG capture devices, it yields a leadfield, i.e., the transfer matrix modelizing the linear relation from sources to capture devices.

OpenMEEG is written entirely in C++, but is usable from Matlab or Python. It is used/integrated in a few software suites for analysis of signals in the brain, such as Brainstorm, Fieldtrip or SPM, ...

Context in which the software is used

Research in medical imagery.

Publications related to the software
  • A. Gramfort, T. Papadopoulo, E. Olivi, M. Clerc. OpenMEEG: opensource software for quasistatic bioelectromagnetics, BioMedical Engineering OnLine 45:9, 2010.

  • Kybic J., Clerc M., Abboud T., Faugeras O., Keriven R., Papadopoulo T., A common formalism for the integral formulations of the forward EEG problem. IEEE Transactions on Medical Imaging, 24:12-28, 2005.

  • See also the software documentation: http://www-sop.inria.fr/athena/software/OpenMEEG/i...

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 23/09/13
  • Minor correction: 23/09/13

gpu-openings : linear opening for GPU/CUDA

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 - janvier 2013
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Pavel Karas, Thierry Grandpierre, Eva Dokladalova, Petr Dokladal
  • Contact designer(s): xkaras1@fi.muni.cz, thierry.grandpierre@esiee.fr, eva.dokladalova@esiee.fr, petr.dokladal@mines-paristech.fr
  • Laboratory, service:

 

General software features

This software implements a fast computing method for openings/closings by large linear morphological structuring element with an arbitrary angle. This method can be adapted to fast granulometry computations on the GPU and CPU. The results are obtained in stream with a single pass over the image, with a minimum of memory used. It is particularly suited to images of high resolution (HD).

Context in which the software is used

This software was used to obtain and validate the results published in the article [1].

Publications related to the software

[1] GPU Implementation of Linear Morphological Openings with Arbitrary Angle, Karas P., Morard V., Bartovsky J., Grandpierre T., Dokladalova E., Matula P., Dokládal P. Journal of Real-Time Image Processing In press, - (2012) - [hal-00680904 - version 1]

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

OpenMVG : C++ library for multi-view geometry in computer vision

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: 0.1 - 08/02/2013
  • License(s): Mozilla Public Licence - V2
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Pierre Moulon
  • Contact designer(s): pmoulon @ gmail.com
  • Laboratory, service:

 

General software features

The library provides solvers for multi-view geometry, from 2 to n views:

  • homography,
  • fundamental matrix,
  • essential matrix,
  • pose estimation,
  • triangulation.

A generic framework allows using these solvers in robust estimation, as RANSAC and AC-RANSAC.

Moreover, a complete algorithmic pipeline for external calibration is provided, as a modern alternative to Bundler software.

The philosophy of this C++ library is to write clear and maintainable code. All modules have unitary tests. It relies on Eigen for linear algebra, Google's Ceres for Levenberg-Marquardt minimization and Lemon for graph processing.

Context in which the software is used

Internally used for multi-view calibration and 3D reconstruction.

Publications related to the software

Adaptive Structure from Motion with a contrario model estimation. Pierre Moulon, Pascal Monasse and Renaud Marlet. Proceedings of ACCV 2012.

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

K-VLD : virtual line descriptor and semi-local graph matching method

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: 20130502 - 02/05/2013
  • License(s): BSD
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): Zhe Liu
  • Contact designer(s): zhe.liu @ enpc.fr
  • Laboratory, service:

 

General software features

From matching interest points between two images, the algorithm finds a set of reliable correspondences using coherency. Virtual straight lines joining interest points in the same image are encoded by a descriptor invariant w.r.t. certain geometric and photometric deformations. This descriptor should be found in virtual lines between corresponding points in another image for ensuring the coherency of both correspondences.

The algorithm is used as a discrimination step between true/false correspondences in the process of rigid or deformable registration and of stereo reconstruction.

Context in which the software is used

Illustration of a research article.

Publications related to the software

Zhe Liu, Renaud MarletVirtual Line Descriptor and Semi-Local Matching Method for Reliable Feature Correspondence.
In 23rd British Machine Vision Conference (BMVC 2012), Surrey, England, September 2012.

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: 22/09/13
  • Minor correction: 22/09/13

OrsaHomography : automatic homographic registration of images

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: 20130522 - 22/05/2013
  • License(s): LGPL
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): Pierre Moulon, Pascal Monasse
  • Contact designer(s): pmo @ mikrosimage.eu
  • Laboratory, service:

 

General software features

This software registers two images by homography. This registration is meaningful in the two following situations:

  • no motion of optical center (only rotation and focal change), or
  • the observed scene is planar (painting, poster, aerial photo from high altitude...)

The software detects SIFT matching candidate points, then it sorts correct and outlier correspondences thanks to a variant of the robust estimation algorithm RANSAC. This variant uses the a contrario framework to estimate automatically the discrimination threshold.

As output, the user gets a list of matching interest points, the homography matrix, registered images, and a panorama built from the registered images by transparency.

Context in which the software is used

This software illustrates the algorithm ORSA, also known as AC-RANSAC, applied to the case of homography estimation.

Publications related to the software

Automatic Homographic Registration of a Pair of Images, with A Contrario Elimination of Outliers
Lionel Moisan, Pierre Moulon, Pascal Monasse
Image Processing On Line (IPOL), 2012.
http://dx.doi.org/10.5201/ipol.2012.mmm-oh

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

Ibex : C++ numerical library based on interval arithmetic and constraint programming

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: 2.0.9 - 28/08/2013
  • License(s): LGPL - v3
  • Status: beta release
  • Support: maintained, ongoing development
  • Designer(s): Ibex team
  • Contact designer(s): gilles.chabert @ mines-nantes.fr
  • Laboratory, service: Universidad Técnica Federico Santa María (Chile)

 

General software features

This C++ library can be used to solve a variety of problems that can be formulated roughly as:

Find a reliable characterization with boxes (Cartesian product of intervals) of sets implicitely defined by constraints.

Where 'reliable' means that all sources of uncertainty should be taken into account, including:

  • approximation of real numbers by floating-point numbers,
  • round-off errors,
  • truncation linearization,
  • model parameter uncertainty,
  • measurement noise,
  • ...
Context in which the software is used

Tool for research in constraint programming.

Publications related to the software
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