logiciels pour le traitement des images IRM en neuro-imagerie; 3D

l'IRM a 30ans donc il existe une pléthore de techniques (issus de la zoologie des séquences de pulses).

Il existe bcp de logiciels de traitement des images IRM:

un des plus "complets" pour les domaines neuro-imagerie anat+fonctionnelle y compris l'animal:
FreeSurfer
http://fr.wikipedia.org/wiki/FreeSurfer
fonctionne sur Mac OS et Linux

Rem: Caret et 3D Slicer peuvent importer des données générées par FreeSurfer...

-Pour le télécharger:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-pour les débutants et wiki:
http://surfer.nmr.mgh.harvard.edu/fswiki
-pour un overview:
http://www.grahamwideman.com/gw/brain/fs/index.htm
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MRIcro:
http://www.mccauslandcenter.sc.edu/mricro/mricro/mricro.html
efficace
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osirix
http://www.osirix-viewer.com/Downloads.html
http://fr.wikipedia.org/wiki/OsiriX

Navigating the Fifth Dimension: Innovative Interface for Multidimensional Multimodality Image Navigation, 2006; doi: 10.1148/rg.261055066
http://radiographics.rsna.org/content/26/1/299.full

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medinria
http://med.inria.fr/

medInria is a multi-platform medical image processing and visualization software. It is free and open-source. Through an intuitive user interface, medInria offers from standard to cutting-edge processing functionalities for your medical images such as 2D/3D/4D image visualization
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brain visa/anatomist
http://brainvisa.info/index_f.html

BrainVISA est distribué avec une boîte à outils dédiée à la segmentation d'images IRM pondérées en T1. Le produit de la principale chaîne de traitements issue de cette boîte à outils est le suivant: une classification gris/blanc pour la morphométrie voxel par voxel, des maillages des surfaces de chaque hémiphère pour la visualisation, des maillages sphériques de la matière blanche de chaque hémisphère, un graphe des plissements corticaux, un étiquetage de ces plissements fondé sur une nomenclature des principaux sillons
You need about 1.5 Gb free disk space to install the BrainVISA pack 4.1. Yes, it's big, but it contains lots of useful things.
Here are the commands to uncompress the package:
On Linux and MacOS:
tar jxvf <brainvisa_package>.tar.bz2
On Windows: unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system).
The package consists of two main programs, anatomist and brainvisa, and a suite of utility programs. All are located in the 'bin' directory of the package. It may be dangerous in a few cases to permanently add this directory to your path, because this can create conflicts with other programs on your system (e.g. python). We suggest two possibilities.
To start a program, type the full path along with the name of the program, e.g.:

  ~/<brainvisa_package>/bin/anatomist
(or create symbolic links to 'anatomist' and 'brainvisa' in a directory listed in your path (maybe /home/yourlogin/bin)

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Afni
http://afni.nimh.nih.gov/afni/
Analysis of Functional NeuroImages
is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
Matlab Library
Ziad Saad and Gang Chen have developed a package of Matlab functions to read, write, and process AFNI datasets. This may be useful for those who want to carry out matlab-based computations such as Dr. Worsley's FMRISTAT or Gang Chen's 4-way ANOVA or user cuddly 3dDeconvolve.
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caret

http://brainvis.wustl.edu/wiki/index.php/Main_Page

Cortical Cartography

(March, 2012) Release of human 'Conte69 atlas' surface-based atlas See Details
Caret software for visualizing and analyzing experimental data on surfaces and volumes
The SumsDB database of published (freely available) and unpublished (private) neuroimaging data. Read more
Webcaret software for online visualization of SumsDB datasets.Read more
Atlases of human, macaque, mouse, and rat that facilitate cross-study comparisons and data mining
Neuroimaging foci. Published stereotaxic coordinates (‘foci’) are especially amenable to data mining. SumsDB currently provides free access to ~25,000 foci from ~800 studies along with tutorials. see also
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en plus de ces rendus surfacique, on peut avoir besoin de maillage.
qualité maillage, un excellent programme:
meshlab
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3D maillages:
import/export http://www.simpleware.com/software/

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-------ImageJ

pour voir les données et pour voir les prétraitements des images, j'aime bien
imageJ avec 3D viewer (plug-in)

Using the 3D viewer as an ImageJ plugin

The ImageJ 3D viewer provides a plugin for ImageJ to visualize image stacks three-dimensionally. The most important features include:

Display stacks as volume renderings, iso-surfaces, orthoslices or surface plots.
Volume editing.
Landmark selection.
Rigid registration, based on manually selected landmarks.
Displaying 4D data.

Using the 3D viewer as a programming library

The viewer can not only be used as an application, but can also be utilized from other Java programs, especially ImageJ plugins, as a library. It offers a well-documented API for high-level 3D visualization.

Displaying an image stack three-dimensional is a matter of a few lines of code:
// Open image
ImagePlus imp = IJ.openImage("/path/to/image");

// Create a universe and show it
Image3DUniverse univ = new Image3DUniverse();
univ.show();

// Add the image as an isosurface
Content c = univ.addVoltex(imp);

--

Point lists

How to create landmarks

How to show and hide landmark points.

How to save and load landmark points.

How to edit them.

Landmark-based registration

How to use landmark points for landmark-based rigid registration

Transformations

How to set and apply transformations in form of matrices

How to save and load transformation matrices

How to avoid unintended object transformation by locking it

How to reset the transformation of an object.

3D Content in PDFs

How to export triangle meshes to a .u3d file or STL file import/export

How to embed the u3d file in a latex file

How to compile it into a pdf containing the 3D data

http://3dviewer.neurofly.de/

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ajouter d'autres plug-in pour la segmentation de base:

Download IntSeg_3D.jar

http://3dviewer.neurofly.de/

part of his thesis

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Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins.
http://en.wikipedia.org/wiki/FIJI_(software)

http://fiji.sc/Fiji
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Neuromodulation at MIT (Boyden); optogenetics : the website for the Synthetic Neurobiology Group

Tools for precision control of neural circuits and complex biological processes

Boyden leads the Synthetic Neurobiology Group
http://syntheticneurobiology.org/people/display/71/11

Activities roughly between 1995 and 2008, and will become increasingly obsolete over time: http://edboyden.org/

http://en.wikipedia.org/wiki/Edward_Boyden

--------projects (DATA@ dec 2011)

Optogenetic molecular reagents enabling control of the activity of targeted neurons and biological functions with light

Optogenetic hardware and systems for control of neural circuits and biological functions with light

Tools for observing and analyzing neural circuit computations and dynamics

Recording and data analysis technologies for observing and analyzing neural circuit dynamics

Exploratory technologies for understanding neural circuits

The analysis and engineering of brain circuit dynamics and function

Understanding how neural circuits compute, drive behaviors, yield brain disorders, and can serve as therapeutic targets

Direct engineering and testing of novel therapeutic platforms for treatment of brain disorders

Ref:
http://syntheticneurobiology.org/projects

optogenetics: a part of neurophotonics

The term "optogenetics" was initially coined in 2006 (Deisseroth 2006) to refer to a rapidly adapted approach of using new high-speed optical methods for probing and controlling genetically targeted neurons within intact neural circuits. More than 500 laboratories around the world are now using optogenetic tools in a broad range of animal models, brain regions, and cell types. Moreover, the field of optogenetics has the capability to not only help explain normal brain function, but also to help explain disease states, and possibly to help inform the development of novel therapeutic strategies for a variety of neurological and psychiatric disorders.
The (re)birth of optogenetics
In a few years time, a small algal protein called channelrhodopsin has made his way up to the spotlights of the Neuroscience research community. Thanks to it, turning on identified cell types in a rapid, reversible and selective manner using light is becoming standard procedure. This technical revolution has been given a name: “optogenetics”, to designate both its use of light and genetic expression strategies. The idea had been in the air for more than 30 years though, and “optogenetic” probes for sensing the brain's electrical and chemical activity had already been developed over the last decade. But the recent development of light-actuated channels and pumps has provided a sudden jolt of energy to the field.
A rapidly evolving field
Within the past 5 years, more than 12 channelrhodopsin variants and 4 light-driven hyperpolarizing pumps have been either cloned or engineered, and around 6 new genetically-encoded calcium sensors have been produced. The arsenal of optogenetic probes is not only improving, but also diversifying in order to serve a wide range of experimental requirements. In parallel, a new savoir-faire is developing to simultaneously deliver light and perform recordings in behaving animals. Companies have already sensed the emergence of a new market and it is easy to bet that “opto-electrodes” will be one of their top products very soon.
The ideas behind OpenOptogenetics.org
OpenOptogenetics.org (OO.o) is a new website which ambitions to provide an online collaborative resource for researcher using optogenetic. The goal of OO.o is to promote, facilitate and democratize the use of optogenetics. OO.o will provide background knowledge, an inventory of available optogenetic probes and their characteristics, tips and protocols, reviews of commercially available equipment and bibliographic references. OO.o is an open wiki, just like Wikipedia. Anyone can register and add content. Therefore OO.o is also an attempt to promote “open research”, where researchers make clear accounts of their methodology and share them with their colleagues without the intermediary of a publication.
OpenOptogenetics.org: a collaborative online resource for “optogeneticists”
Link :http://www.openoptogenetics.org


French Lab.

Several laboratories are currently employing optogenetic approaches:
Bordeaux: the laboratories of Erwan Bezard (to dissect basal ganglia functions) and Christophe Mulle (CNRS 5091)
Paris: College de France: Vandecasteele Marie.

...

ESFRI, the European Strategy Forum on Research Infrastructures; an example: euro-bioImaging

ESFRI, the European Strategy Forum on Research Infrastructures, is a strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach. The competitive and open access to high quality Research Infrastructures supports and benchmarks the quality of the activities of European scientists, and attracts the best researchers from around the world.

The mission of ESFRI is to support a coherent and strategy-led approach to policy-making on research infrastructures in Europe, and to facilitate multilateral initiatives leading to the better use and development of research infrastructures, at EU and international level.

ESFRI’s delegates are nominated by the Research Ministers of the Member and Associate Countries, and include a representative of the Commission, working together to develop a joint vision and a common strategy. This strategy aims at overcoming the limits due to fragmentation of individual policies and provides Europe with the most up-to-date Research Infrastructures, responding to the rapidly evolving Science frontiers, advancing also the knowledge-based technologies and their extended use.

Since it was formed in 2002 at the behest of the European Council, ESFRI has witnessed significant advances towards unity and international impact in the field of research infrastructures. The publication of the first Roadmap for pan-European research infrastructures in 2006, and its update in 2008 was a key contributing factor, and several projects are now entering the realization phase. The Forum is determined to sustain the momentum in the implementation of the projects on the Roadmap, to expand the outreach to those scientific fields which are still evolving their conceptual approach in this direction, and to increase the involvement of all Countries by developing ad-hoc Regional policies. A further update of the ESFRI Roadmap, focusing on Energy, Food and Biology, will be published at the end of 2010, to coincide with a Conference to be held under the Belgian Presidency of the EU.

To keep Europe at the rapidly evolving forefront of science and technology, and to increase the capacity to meet the needs of the EU and World scientific community, much remains to be done: ESFRI looks forward to the challenging times ahead.
Ref: http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=esfri

---------------an example:
http://www.eurobioimaging.eu/

Deep in vivo two-photon imaging of blood vessels; doi 2011; J-C Vial UMR Grenoble

Deep in vivo two-photon imaging of blood vessels with a new dye encapsulated in pluronic nanomicelles | Current Issue - Journal of Biomedical Optics:

Mathieu Maurin, Olivier Stéphan, Jean-Claude Vial, Seth R. Marder and Boudewijn van der Sanden,

"Deep in vivo two-photon imaging of blood vessels with a new dye encapsulated in pluronic nanomicelles
J. Biomed. Opt. 16, 036001 (Mar 01, 2011);

doi:10.1117/1.3548879"