You can find the documentation of the toolbox on brainvisa web site.
BrainRAT results from collaborative work of image processing methodologists and biologists of MIRCen, a new CEA facility headed by Philippe Hantraye and dedicated to preclinical research.
BrainRAT is mainly developed by the MIRCen image processing team of Thierry Delzescaux, PhD (Julien Dauguet, PhD, Jessica Lebenberg, PhD student, N. Souedet, software engineer and Didier Thenadey, IT specialist) as well as by some close collaborators (Albertine Dubois, PhD, Inserm U803, Vincent Frouin, CEA/SCSR, Denis Rivière, PhD and Yann Cointepas, PhD, CEA/NeuroSpin).
Expert biologists have been associated with this project, from the beginning, to guarantee the relevance of developed methods and the compatibility/performances of processing times with biological experiments (Anne-Sophie Hérard, PhD, Gilles Bonvento, PhD, and Françoise Condé, PhD).
All the above-mentioned people can be contacted by e-mail at firstname.lastname@example.org.
BrainRAT's goal is to provide an automated and generic toolbox for the processing of histological and autoradiographic sections based on a two-step approach, which involves:
At the beginning, these methods have been developed to analyse autoradiographic data in 3D using complementary histological information. The 3D reconstruction of biological volumes arising from several histological and/or autoradiographic sections enables to take advantage of the high resolution of ex vivo autoradiography as well as of the diversity of available histological stainings.
The analysis of autoradiographic data, 3D reconstructed or not, remains traditionally limited to conventional region of interest (ROI)-based analysis. Although the users have the corresponding histological stained sections available to consider anatomical information, the delineation of ROI(s) to be analyzed is usually directly performed on the autoradiographic sections, which may be inaccurate and subject to observer bias. To overcome this limitation, BrainRAT enables to perform multimodal co-registration between slices or 3D reconstructed volumes.
Recent studies have highlighted the ability of voxel-wise statistical analysis to deal with 3D reconstructed autoradiographic volumes for group comparisons. This automated, exploratory, whole-brain approach can be used to analyze local functional differences between population groups without the need for prior assumptions. BrainRAT provides useful tools to carry out such studies in optimal conditions (optimized digitization, 3D reconstruction algorithms, activity conversion and intensity normalization procedures).
These methods have been applied to Nissl stained (cresyl violet) sections and [14C]-2DG autoradiography and intensively validated both in rats and mice. They have been also successfully tested on other post mortem imaging modalities such as immunohistochemistry, fluorescence, etc. They could now be extended to various biological applications (activation models, morphology, lesion extension, development, etc.) and to domains of application including pathological and therapeutic studies involving animal models of various brain diseases (neurodegenerative diseases, ischemia, and cancer).
For the time being, the only reference to BrainRAT is related to proceedings of the SFN 2008:
BrainRAT: Brain Reconstruction and Analysis Toolbox. A freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents.
A. Dubois, J. Dauguet, N. Souedet, A.-S. Hérard, D. Rivière, Y. Cointepas, G. Bonvento, P. Hantraye, V. Frouin, T. Delzescaux. In Proc. 38th annual meeting of the Society for Neuroscience, Washington, USA, 2008.
The main reference relating to the computerized treatments and procedures gathered in BrainRAT to be mentioned is:
Automated three-dimensional analysis of histological and autoradiographic rat brain sections: application to an activation study.
A. Dubois, J. Dauguet, A-S. Hérard, L. Besret, E. Duchesnay, V. Frouin, P. Hantraye, G. Bonvento and T. Delzescaux. Journal of Cerebral Blood Flow and Metabolism, 2007, 27(10), 1742-1755. Abstract.
Yet, these developments were the basis of other works published by our team:
They enabled to provide evidence that the metabolic response to synaptic activation (i.e. enhancement of glucose uptake) is decreased in the superior colliculus during visual stimulation in young adult mice deficient for the glial glutamate transporter GLT-1 (Figure 1.1).
Decreased metabolic response to visual stimulation in the superior colliculus of mice lacking the glial glutamate transporter GLT-1.
A-S. Herard, A. Dubois, C. Escartin, K. Tanaka, T. Delzescaux, P. Hantraye and G.Bonvento. European Journal of Neuroscience, 2005, 22(7):1807-11. Abstract.
They enabled to accurately study stimulus-driven synaptic activity in vivo in a restricted rat brain region, the superior colliculus (Figure 1.2).
siRNA targeted against amyloid precursor protein impairs synaptic activity in vivo.
A-S. Hérard, L. Besret, A. Dubois, J. Dauguet, T. Delzescaux, P. Hantraye, G. Bonvento and K.L. Moya. Neurobiology of Aging, 2006, 27(12):1740-50. Abstract.
They also enabled the investigation of new methods of analysis of 3D biologic data in groups of rodents, based on voxel-wise statistical approaches without the need for prior assumptions (Figure 1.3).
Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes: application to unilateral visual stimulation.
A. Dubois, A-S. Hérard, E. Duchesnay, G. Flandin, L. Besret, P. Hantraye, G. Bonvento and T. Delzescaux. NeuroImage, 2008, 40(2), 482-494. Abstract.
Lastly, these developments were also the basis of works performed in collaboration with other teams :
Metabolic and vascular changes induced in mice olfactory glomeruli by odor presentation (Figure 1.4).
Gurden et al. IMNC, UMR8165 CNRS-University of Paris 7 and Paris 11, Orsay, France. 5th Forum of European Neuroscience (FENS), Vienna, Austria, 2006.
The next releases of BrainRAT toolbox will contain new processes allowing to:
BrainRAT toolbox is a BrainVISA add-on module package providing additional processes and functionalities relating to 3D reconstruction and analysis of post mortem rodent brain sections.
BrainVISA, in-house image processing software, is already available for free download on the Internet (http://brainvisa.info). Since then, the core of BrainVISA is mainly developed in CEA/NeuroSpin by the LNAO lead by Jean-François Mangin, PhD (Yann Cointepas, PhD and D. Rivière, PhD) and by software engineers of the IFR 49 (Isabelle Denghien and Dominique Geffroy). The first prototype was developed by Yann Cointepas during years 2000/2001. BrainVISA also relies on Anatomist software visualization capacities.
Anatomist has been designed in the Service Hospitalier Frederic Joliot of CEA and is now mainly developed by Denis Rivière, PhD. The current version stems from ten years of work on several prototypes. One of its main original features is the generic module dedicated to structural data, namely sets of objects linked one another into a graph structure. It also provides a toolbox for regions of interest manual drawing.
For a complete and more detailed description of BrainVISA software, please refer to the handbook of BrainVISA.
If you have any problems or queries relating to BrainRAT, BrainVISA or Anatomist, please contact us through the BrainVISA forum at: http://brainvisa.info/forum.
Yet, before asking questions of reporting problems, please make sure your query is not solved in the FAQ. Thank you to consider that we have very few resources for technical support at the moment.
If you have any problems with your data, please check the procedure described in the How to scan section.
For training and educational purposes, 2 datasets can be downloaded on demand at the following e-mail address: email@example.com. Please mention your institution, lab, research area, email address and operating system (Windows, MacOS or Linux).
Demonstration data enable to test all the BrainRAT functionalities through two applications: