Archive for the 'format-fichiers' Category web-based, platform-independent, multi-user interface for managing scientific literature & citations


refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI & COinS metadata allow for easy access by clients and search engines. Please see our Feature highlights page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given here.


You can download the stable release version of refbase from the SourceForge download page. Please see the instructions on how to install or update refbase. The latest source code can be checked out and installed from the refbase Subversion repository.

refbase 0.9.5 README

About refbase
refbase is a web-based solution for managing scientific literature,
references and citations.

Currently, the following features have been implemented for:
– search the database using different search forms
– search within results
– browse found records and sort results by any database field
– view results in different views (list view, citations, details,
print view)
– display results in different citation styles & output formats
– export selected records to XML (Atom, MODS, OAI_DC, ODF) and (via
the GPLed Bibutils programs) to ADS, BibTeX, EndNote, ISI, RIS and
Word XML
– display rich text (i.e., italics, super/sub-script, greek letters)
– extract citations from a text & build an appropriate reference list
– track additions via RSS and generate custom RSS feeds from searches
– web services (SRU & OpenSearch) that allow clients to access a
refbase database using a standard query syntax and retrieve results
in structured XML format
– dissemination of bibliographic data via standard methods (COinS &
unAPI) allowing clients to automatically discover and extract data
from refbase
– search a refbase online database from the command line and retrieve
results in various export & citation formats
– user-specific fields which are stored individually for each user
– import of records from common bibliographic formats and online
databases via the web interface or the command line
– automatic email announcements for newly added records
– save and recall search queries
– adding records to user-specific groups
– add/edit/delete records as well as file upload & download links
– user management interface provided to the database admin
– set access permissions on a per-user basis

More information is given at:


refbase requires:
– a web server (like the Apache HTTP Server <;)
– PHP <; (version 4.4.0 or greater) with enabled
session support & installed PHP MySQL module
– MySQL <; (version 4.1.x or greater required for
Unicode support)

– for import and export of various formats (e.g., Endnote & BibTeX):
Bibutils <;
(version 3.21 or greater)

More detailed information is available at:

ParaView is an application framework as well as a turn-key application; Modeling software OpenFOAM and ParaView ; mesh processing: generation, manipulation, conversion

ParaView is an open source, multi-platform data analysis and visualization application. It has a client-server architecture to facilitate remote visualization of datasets

It is an application built on top of the Visualization Tool Kit (VTK) libraries.

The ParaView code base is designed in such a way that all of its components can be reused to quickly develop vertical applications. This flexibility allows ParaView developers to quickly develop applications.

Input/Output and File Format

  • Supports a variety of file formats including: VTK (new and legacy, all types including parallel, ascii and binary, can read and written).
  • Various polygonal file formats including STL and BYU (by default, read only, other VTK writers can be added by writing XML description).
  • Many other file formats are supported. See ParaView Readers and ParaView Writers for a full list.

CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. ParaView utilizes CMake for the software compilation process.


ParaView is used as the visualization platform for the Modeling software OpenFOAM (Open Field Operation and Manipulation).It is primarily a C++ toolbox for the customisation and extension of numerical solvers for continuum mechanics problems, including computational fluid dynamics (CFD). It comes with a growing collection of pre-written solvers applicable to a wide range of problems.

First major general-purpose CFD package to use polyhedral cells. This functionality is a natural consequence of the hierarchical description of simulation objects.

OpenFOAM compares favourably with the capabilities of most leading general-purpose commercial closed-source CFD packages. It relies on the user’s choice of third party pre- and post-processing utilities, and ships with:

  • a plugin (paraFoam) for visualisation of solution data and meshes in ParaView.
  • a wide range of mesh converters allowing import from a number of leading commercial packages
  • an automatic hexahedral mesher to mesh engineering configurations

OpenFOAM was conceived as a continuum mechanics platform but is ideal for building multi-physics simulations.

OpenCFD develop OpenFOAM in the Linux/UNIX operating system because: we believe it is the best platform for this kind of high end simulation code development and operation; Linux is efficient, robust, reliable and flexible and undergoes rapid development and improvement; Linux is open source, like OpenFOAM; Linux is very effective for parallel operation on Beowulf clusters.

OpenFOAM is open source software so people can freely compile it on any operating system they choose. Most OpenFOAM users are running Linux, so this site offers the download of binaries for selected Linux systems.

As the present time we are unaware of any binary distributions for Windows or MacOSX. However, ports to these operating systems have been the subject of debate on the OpenFOAM discussion site, which may provide the best source of information on the matter.

OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells.

Mesh generation

OpenFOAM applications handle unstructured meshes of mixed polyhedra with any number of faces: hexahedra, tetrahedra, degenerate cells, basically anything.

Mesh generation is made simple by the fact that a cell is simply represented as a list of faces and a face as a list of vertices: this makes mesh handling very easy even for complex meshes with, say, embedded refinement or complex shapes near the boundary.

OpenFOAM is supplied with the following mesh generator tools that run in parallel.

Mesh generation tools

blockMesh A multi-block mesh generator
extrude2DMesh Takes 2D mesh (all faces 2 points only, no front and back faces) and creates a 3D mesh by extruding with specified thickness
extrudeMesh Extrude mesh from existing patch (by default outwards facing normals; optional flips faces) or from patch read from file
snappyHexMesh Automatic split hex mesher. Refines and snaps to surface

The main mesh generators cover two extremes: snappyHexMesh, that can mesh to complex CAD surfaces; blockMesh a simple file-driven block mesh generator.

Mesh manipulation

OpenFOAM is supplied with several utilties that perform mesh checking and manipulation. The full list of utilties is given below

Mesh manipulation

attachMesh Attach topologically detached mesh using prescribed mesh modifiers
autoPatch Divides external faces into patches based on (user supplied) feature angle
cellSet Selects a cell set through a dictionary
checkMesh Checks validity of a mesh
createBaffles Makes internal faces into boundary faces. Does not duplicate points, unlike mergeOrSplitBaffles
createPatch Utility to create patches out of selected boundary faces. Faces come either from existing patches or from a faceSet
deformedGeom Deforms a polyMesh using a displacement field U and a scaling factor supplied as an argument
faceSet Selects a face set through a dictionary
flattenMesh Flattens the front and back planes of a 2D cartesian mesh
insideCells Picks up cells with cell centre ’inside’ of surface. Requires surface to be closed and singly connected
mergeMeshes Merge two meshes
mergeOrSplitBaffles Detects faces that share points (baffles). Either merge them or duplicate the points
mirrorMesh Mirrors a mesh around a given plane
moveDynamicMesh Mesh motion and topological mesh changes utility
moveEngineMesh Solver for moving meshes for engine calculations.
moveMesh Solver for moving meshes
objToVTK Read obj line (not surface!) file and convert into vtk
pointSet Selects a point set through a dictionary
refineMesh Utility to refine cells in multiple directions
renumberMesh Renumbers the cell list in order to reduce the bandwidth, reading and renumbering all fields from all the time directories
rotateMesh Rotates the mesh and fields from the direcion n1   \special {t4ht= to the direction n2   \special {t4ht=
setSet Manipulate a cell/face/point set interactively
setsToZones Add pointZones/faceZones/cellZones to the mesh from similar named pointSets/faceSets/cellSets
splitMesh Splits mesh by making internal faces external. Uses attachDetach
splitMeshRegions Splits mesh into multiple regions
stitchMesh ’Stitches’ a mesh
subsetMesh Selects a section of mesh based on a cellSet
transformPoints Transforms the mesh points in the polyMesh directory according to the translate, rotate and scale options
zipUpMesh Reads in a mesh with hanging vertices and zips up the cells to guarantee that all polyhedral cells of valid shape are closed

Mesh motion

OpenFOAM adopts a novel approach to mesh motion by defining it in terms of the boundary motion which is extremely robust.

The solver need only define the the motion of the boundary and everything else will be done automatically. The open architecture of OpenFOAM solver codes allows quick and efficient implementation: mesh motion can be based on any solution variable, either local or integrated and by dynamically adjusted during the run.

Mesh motion is also transparently integrated with top-level models: the model writer does not see the additional complexity, which is conveniently packaged within the discretisation operators.

For examples of automated mesh motion in OpenFOAM, see Solutions

Mesh conversion

OpenFOAM accepts meshes generated by any of the major mesh generators and CAD systems. Listed below are converter utlities for the major commercial mesh generators. Note that it is also possible to import the meshes from most general purpose mesh generators since they will export in a format read by one of the converters.

Mesh converters

ansysToFoam Converts an ANSYS input mesh file, exported from I-DEAS, to OPENFOAM®format
cfx4ToFoam Converts a CFX 4 mesh to OPENFOAM®format
fluent3DMeshToFoam Converts a Fluent mesh to OPENFOAM®format
fluentMeshToFoam Converts a Fluent mesh to OPENFOAM®format including multiple region and region boundary handling
foamMeshToFluent Writes out the OPENFOAM®mesh in Fluent mesh format
foamToStarMesh Reads an OPENFOAM®mesh and writes a PROSTAR (v4) bnd/cel/vrt format
gambitToFoam Converts a GAMBIT mesh to OPENFOAM®format
gmshToFoam Reads .msh file as written by Gmsh
ideasUnvToFoam I-Deas unv format mesh conversion
kivaToFoam Converts a KIVA grid to OPENFOAM®format
mshToFoam Converts .msh file generated by the Adventure system
netgenNeutralToFoam Converts neutral file format as written by Netgen v4.4
plot3dToFoam Plot3d mesh (ascii/formatted format) converter
polyDualMesh Calculate the dual of a polyMesh. Adheres to all the feature and patch edges
sammToFoam Converts a STAR-CD SAMM mesh to OPENFOAM®format
star4ToFoam Converts a STAR-CD (v4) PROSTAR mesh into OPENFOAM®format
starToFoam Converts a STAR-CD PROSTAR mesh into OPENFOAM®format
tetgenToFoam Converts .ele and .node and .face files, written by tetgen
writeMeshObj For mesh debugging: writes mesh as three separate OBJ files which can be viewed with e.g. javaview

The algorithms below are ready to be downloaded. Biomedical Imaging Group. EPFL

Available Algorithms

The algorithms below are ready to be downloaded. They are generally written in JAVA or in ANSI-C, either by students or by the members of the Biomedical Imaging Group.Please contact the author of the algorithms if you have a specific question.
JAVA: Plug-ins for ImageJ
JAVA classes are usually meant to be integrated into the public-domain software ImageJ.
bullet Drop Shape Analysis. New method based on B-spline snakes (active contours) for measuring high-accuracy contact angles of sessile drops.
bullet Extended Depth of Focus. The extended depth of focus is a image-processing method to obtain in focus microscopic images of 3D objects and organisms. We freely provide a software as a plugin of ImageJ to produce this in-focus image and the corresponding height map of z-stack images.
bullet Fractional spline wavelet transform. This JAVA package computes the fractional spline wavelet transform of a signal or an image and its inverse.
bullet Image Differentials. This JAVA class for ImageJ implements 6 operations based on the spatial differentiation of an image. It computes the pixel-wise gradient, Laplacian, and Hessian. The class exports public methods for horizontal and vertical gradient and Hessian operations (for those programmers who wish to use them in their own code).
bullet MosaicJ. This JAVA class for ImageJ performs the assembly of a mosaic of overlapping individual images, or tiles. It provides a semi-automated solution where the initial rough positioning of the tiles must be performed by the user, and where the final delicate adjustments are performed by the plugin.
bullet NeuronJ. This Java class for ImageJ was developed to facilitate the tracing and quantification of neurites in two-dimensional (2D) fluorescence microscopy images. The tracing is done interactively based on the specification of end points; the optimal path is determined on the fly from the optimization of a cost function using Dijkstra’s shortest-path algorithm. The procedure also takes advantage of an improved ridge detector implemented by means of a steerable filterbank.
bullet PixFRET. The ImageJ plug-in PixFRET allows to visualize the FRET between two partners in a cell or in a cell population by computing pixel by pixel the images of a sample acquired in three channels.
bullet Point Picker. This JAVA class for ImageJ allows the user to pick some points in an image and to save the list of pixel coordinates as a text file. It is also possible to read back the text file so as to restore the display of the coordinates.
bullet Resize. This ImageJ plugin changes the size of an image to any dimension using either interpolation, or least-squares approximation.
bullet SheppLogan. The purpose of this ImageJ plugin is to generate sampled versions of the Shepp-Logan phantom. Their size can be tuned.
bullet Snakuscule. The purpose of this ImageJ plugin is to detect circular bright blobs in images and to quantify them. It allows one to keep record of their location and size.
bullet SpotTracker Single particle tracking over noisy images sequence. SpotTracker is a robust and fast computational procedure for tracking fluorescent markers in time-lapse microscopy. The algorithm is optimized for finding the time-trajectory of single particles in very noisy image sequences. The optimal trajectory of the particle is extracted by applying a dynamic programming optimization procedure.
bullet StackReg. This JAVA class for ImageJ performs the recursive registration (alignment) of a stack of images, so that each slice acts as template for the next one. This plugin requires that TurboReg is installed.
bullet Steerable feature detectors. This ImageJ plugin implements a series of optimized contour and ridge detectors. The filters are steerable and are based on the optimization of a Canny-like criterion. They have a better orientation selectivity than the classical gradient or Hessian-based detectors.
bullet TurboReg. This JAVA class for ImageJ performs the registration (alignment) of two images. The registration criterion is least-squares. The geometric deformation model can be translational, conformal, affine, and bilinear.
bullet UnwarpJ. This JAVA class for ImageJ performs the elastic registration (alignment) of two images. The registration criterion includes a vector-spline regularization term to constrain the deformation to be physically realistic. The deformation model is made of cubic splines, which ensures smoothness and versatility.
Most often, the ANSI-C pieces of code are not a complete program, but rather an element in a library of routines.
bullet Affine transformation. This ANSI-C routine performs an affine transformation on an image or a volume. It proceeds by resampling a continuous spline model.
bullet Registration. This ANSI-C routine performs the registration (alignment) of two images or two volumes. The criterion is least-squares. The geometric deformation model can be translational, rotational, and affine.
bullet Shifted linear interpolation. This ANSI-C program illustrates how to perform shifted linear interpolation.
bullet Spline interpolation. This ANSI-C program illustrates how to perform spline interpolation, including the computation of the so-called spline coefficients.
bullet Spline pyramids. This software package implements the basic REDUCE and EXPAND operators for the reduction and enlargement of signals and images by factors of two based on polynomial spline representation of the signal.
bullet E-splines. A Mathematica package is made available for the symbolic computation of exponential spline related quantities: B-splines, Gram sequence, Green function, and localization filter.
bullet Fractional spline wavelet transform. A MATLAB package is available for computing the fractional spline wavelet transform of a signal or an image and its inverse.
bullet Fractional spline and fractals. A MATLAB package is available for computing the fractional smoothing spline estimator of a signal and for generating fBms (fractional Brownian motion). This spline estimator provides the minimum mean squares error reconstruction of a fBm (or 1/f-type signal) corrupted by additive noise.
bullet Hex-splines : a novel spline family for hexagonal lattices. A Maple 7.0 worksheet is available for obtaining the analytical formula of any hex-spline (any order, regular, non-regular, derivatives, and so on).
bullet MLTL deconvolution : This Matlab package implements the MultiLevel Thresholded Landweber (MLTL) algorithm, an accelerated version of the TL algorithm that was specifically developped for deconvolution problems with a wavelet-domain regularization.
bullet OWT SURE-LET Denoising : This Matlab package implements the interscale orthonormal wavelet thresholding algorithm based on the SURE-LET (Stein’s Unbiased Risk Estimate/Linear Expansion of Thresholds) principle.
bullet WSPM : Wavelet-based statistical parametric mapping, a toolbox for SPM that incorporates powerful wavelet processing and spatial domain statistical testing for the analysis of fMRI data.

FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FreeSurfer is brought to you by the Athinoula A. Martinos Center for Biomedical Imaging. Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute and is part of the National Alliance for Medical Image Computing (NA-MIC) funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

FreeSurfer Beginners Guide

FreeSurfer is a freely available software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging used for a number of procedures including:

  1. Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. link
  2. Processing of functional magnetic resonance imaging (fMRI) data. link
  3. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. link
  4. Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions. link

Machine Requirements

To run FreeSurfer, you will need either a PC running Linux or a Macintosh running OS X.

FreeSurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run FreeSurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons with 4 to 8 GB of DDR SDRAM, and 250GB of disk space.


The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer’s volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describe some of FreeSurfer’s tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:

  • perform surface reconstructions;
  • generate subcortical segmentations;
  • fix errors encountered during the volume or surface processing;
  • overlay functional data onto surfaces;
  • perform group analysis of structural (e.g. thickness) and functional data.

code; matlab; mesh; Source Signal Imaging, developers of EMSE Suite. EMSE Suite is a Windows-based software toolkit for 4D multimodal functional brain imaging

Welcome to Source Signal Imaging, developers of EMSE Suite. EMSE Suite is a Windows-based software toolkit for 4D multimodal functional brain imaging, including analysis, source estimation, image processing, and visualization. MEG/EEG and MRI/fMRI datasets from many vendors and standard formats may be combined to obtain results not available from independent analyses of the separate modalities. First introduced in 1996, and now used by clinicians and researchers worldwide, EMSE Suite has a modular architecture, rich feature set and relatively low cost. Click on the menu to the left to find information about our products, news of upcoming events, links to other sites of interest, as well as access to original publications.

EMSE 5.3 Release Candidate 3 is here
6.22.09 We have added many new features and improvements

Mesh Generation using Matlab ; mesh generator, 2D and 3D;

Mesh Generation using Matlab

These days most of the research in the field of fluids, structures, porous media, brain computer interfacing you name it, uses numerical simulations. Reason: It is much cheaper and many times faster compared to experiments. Mesh Generation forms an integral part of numerical analysis/simulation.
Although, there are plenty of commercial softwares based on Finite Element Methods and Finite Volume Methods like COMSOL, FLEUNT, ANSYS, NUMECA and many more with exceptional Mesh/Grid Generation features (amira).
But many times its difficult to use the meshes generated by these softwares which suits to your particular simulation need.
Reason: Many of the exsiting software don’t have this feature where you can create a mesh and use it some which have such features requires you to do some complicated modifications in your code to import these meshes. There are although loads of mesh generator available some of which open source and free to download.
But, then again problem comes does these free source code suits your purpose. I encountred this problem over the last couple of months.
I am doing research in the field of Petroleum Reservoir Simulation and I need to test a lot of numerical examples on different sorts of meshes/grids in 2 and 3D. I do most of my simulation work in MATLAB, some people might argue that MATLAB is slow and all sorts of reason about other programming languages are faster like C++ and Fortran. I don’t deny that fact but on the other hand the library of existing function which matlab has is amazing and its Array handling feature and sparse code it amazing too. The only and important reason I use MATLAB is its capability to handle array operations.
{In my simulation code I have to solve at times 9 simulatneous equations in 2D and 27 equations in 3D, which maximizes use of array operations. I also frequently use MAPLE to do my algebra and other good thing about MATLAB is that I can directly import the MAPLE algebra in Array Format into MATLAB which suits my purpose}

Now comming to the meshes in MATLAB, try doing a google on ‘meshes in MATLAB’ or ‘grid generation in 2 and 3D in MATLAB’, a invested a lot of time to find some unseful source code in matlab searching on google groups etc the only useful package I found was by Per-Olof Persson titled ‘DistMesh – A Simple Mesh Generator in MATLAB’.



No doubt its an amazing piece of work but again it didnt realy suits my purpose. The reason being I needed unstructured meshes of different element types in 3D like prisms, hex, tetra and pyramids. In 2D also I needed meshes which are boundary aligned to control volume and are matching to the underlying medium.

So, What next ? I started from scratch and now I have come up with stand alone code in MATLAB which has functionality to create different kind of meshes in 2D and 3D. These are structured and Unstructured meshes, perturbed and bondary aligned too. If any one is in need of such meshes in 2 and 3D please have a look at:

Then you can drop me an email and I will get back to you and will help you and if required will also provide you with the source code if it suits your purpose.


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