Available Algorithms  
The algorithms below are ready to be downloaded. They are generally written in JAVA or in ANSIC, 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.  

Archive for the 'matlab' Category
The algorithms below are ready to be downloaded. Biomedical Imaging Group. EPFL
Published 9 octobre 2009 ANSIC , formatfichiers , imageJ , mathematica , matlab , neuroInformatics , outils4programmation , traitement d'image 1 Commentcode; matlab; mesh; Source Signal Imaging, developers of EMSE Suite. EMSE Suite is a Windowsbased software toolkit for 4D multimodal functional brain imaging
Published 9 octobre 2009 3D , formatfichiers , matlab , soft_interessant Leave a CommentWelcome to Source Signal Imaging, developers of EMSE Suite. EMSE Suite is a Windowsbased 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, literate programming, matlab; mathematica; persson
Published 8 octobre 2009 bibliography , mathematica , matlab , mesh generation 1 Commenthttp://library.wolfram.com/infocenter/MathSource/5475/
This Mathematica notebook is an effort to transcribe the MATLAB code of a 2D mesh generation algorithm as described explicitly in Persson and Strang’s paper [1]. The goal is to make the algorithm executable in Mathematica so that its users can also experiment with the algorithm.
Since the algorithm was expressed very clearly from their original paper [1] including the MATLAB code, which is a perfect example of literate programming in MATLAB, it is pretty easy to translate the MATLAB code « literally » into Mathematica. Such translation is virtually always possible in either direction even without human interference. And such a Rosetta Stone kind of translation might be useful if one species of people coding in either MATLAB or Mathematica were to disappear, future generations would still be able to rediscover one programming language by reading its interpretation in the other one.
However, it is so tempting to present the literate programming capability of Mathematica by following its general principles; that is, (a) documentation mingles with code and both get prettyprinted; (b) shuffle code pieces for human readability. I decided to transcribe the code manually.
The original MATLAB code was documented as 8 steps (sections) in sequential order, which is easy to follow because the ideas behind the code were explained beforehand in early parts of the paper. So it is recommended that you read part 1 and 2 of the original paper. Instead of following the MATLAB code literally in 8 steps, this notebook breaks the code pieces apart and examines each of them separately.
finite element; matlab
Published 8 octobre 2009 bibliography , finite volume , matlab Leave a CommentKwon, Y. W. and Bang, H. The Finite Element Method Using MATLAB. Boca Raton, FL: CRC Press, 1996
Mesh Generation using Matlab ; mesh generator, 2D and 3D;
Published 8 octobre 2009 3D , formatfichiers , matlab , mesh generation 6 CommentsNow 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 PerOlof Persson titled ‘DistMesh – A Simple Mesh Generator in MATLAB’.
YES!
see: http://persson.berkeley.edu/software.html
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.
http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=10307&objectType=FILE
matlab and amira; how to integrate complex calculus into Amira using MATLAB
Published 6 octobre 2009 3D , amira , matlab 2 Commentshttp://www.amiravis.com/documentation/521/amira/usersguide/tutmatlab.html
2.14 Using MATLAB Scripts
In this tutorial you will learn how to integrate complex calculus into Amira using MATLAB (The MathWorks, Inc) by the means of the CalculusMatlab module.
In order to use the CalculusMatlab module, MATLAB 7 must be correctly installed on your computer. The CalculusMatlab module establishes a connection to the MATLAB computational engine that was registered during installation. If you did not register during installation, on the Windows command line you can enter the command:
 matlab /regserver
The limitations of the CalculusMatlab module are listed in its documentation.
This tutorial covers the following topics:
 Loading and executing a MATLAB script.
 Lowpass filtering on images.
 Controlling the script with a time slider.
 Thresholding on a volume.
2.14.1 Lowpass Filtering on Images
In this section we will learn how to apply a lowpass filter on an Amira image using the MATLAB Fourier transformation. This example shows how to pass data and control variables from Amira to MATLAB, execute a MATLAB script, and import the data back into Amira
.
 Load the lena.png image file located in subdirectory data/tutorials/matlab.
 Choose Luminance in the Channel Conversion field as shown in Figure 34.
 Right click on the green icon and choose CalculusMatlab from the Compute section.
A new red icon appears, the CalculusMatlab module that will try to connect to the MATLAB engine. This may take a while.
Figure 34: Loading the image 
 Load the script lowpass.m located in subdirectory data/tutorials/matlab by clicking the Read button of the File port.
 Execute the script by clicking on the buffer button of the Execute port.
 Connect an OrthoSlice to the filtered image result.
The module uses the MATLAB computation engine which has its own user interface.
You can easily show or hide the MATLAB console using the checkbox in the options field. The MATLAB console is very useful for debugging purposes because it allows you to access variables of the MATLAB workspace. Any variable not cleared by the MATLAB « clear » command in the script is accessible in the MATLAB workspace, even after finishing the current CalculusMatlab computation (see the CalculusMatlab documentation).
Figure 35: The CalculusMatlab module 
In addition you can control scalar parameters of the script using time sliders:
 Create a time slider (File/Create/Data/Time).
 Connect the CalculusMatlab module to the time slider.
 Change the line cutoff=0.05 to cutoff=t in the script (see the CalculusMatlab documentation for more information about the keyword t).
 Click on the time slider and adjust the value that will be assigned to w. Right mouse click in the text field of the time slider and select Configure to adjust the data range of the parameters.
Figure 36: Left: original Right: lowpass filtered 
Note: To handle RGBA image filtering, you must load the image with Color Field Channel Conversion and treat each channel separately in the script.
2.14.2 Thresholding on a Volume
In this section we will learn how to apply a threshold to a volume. This is done by setting a value for a threshold. If the value for the voxel is less than the threshold, the voxel value is assigned the value of zero. If it is above the threshold, it is assigned a value of 255.
 Load the file lobus.am located in subdirectory data/tutorials.
 Right click on the green icon and choose CalculusMatlab from the Compute section.
 Load the script threshold.m located in subdirectory data/tutorials/matlab by clicking the Read button of the File port.
 Execute the script by clicking on the buffer button of the Execute port.
A new green icon appears, the Lattice that will hold the threshold result. Connect an OrthoSlice or a Voltex to see the result.
Note: Any variable accessed by MATLAB and pushed back into the Amira workspace will lose its voxel size information. You will need to correct the voxel size manually using the Crop Editor.
U3D and matlab file exchange; Export triangulated mesh into a pdf with a 3D interactive object.
Published 6 octobre 2009 3D , acrobat , formatfichiers , freeware , matlab , outils4programmation Leave a Commenthttp://www.mathworks.com/matlabcentral/fileexchange/25383
Description 
Export triangulated mesh into a pdf with a 3D object. The matlab mesh is converted to IDTF with matlab code. The IDTF file is converted to u3d with an external binary file. The u3d file can then be embedded into a pdf with pdflatex and the movie15 package. The user can then interact with the mesh (zoom, rotate etc.) from adobe reader. The package contains demo data and example of output. The code of the IDTF to U3D converter can be obtained at : http://sourceforge.net/projects/u3d/ The toolbox has been tested on mac intel, linux and windows. To test run the script : demo_mesh2pdf.m 
MATLAB release  MATLAB 7 (R14) 
Other requirements  The windows version requires to install MeshLab : http://meshlab.sourceforge.net/ 
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