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. 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.Figure 1.1. (Left) 3-D reconstruction of cresyl violet-stained sections clearly outlines the superior colliculus. (Right) The corresponding 3-D reconstruction of autoradiographic images indicates the extent of the metabolic activation during checkerboard stimulation in a control C57BL/6 mouse with one eye shut and one eye open.
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.Figure 1.2. 3-D reconstruction of the left and right manually segmented superior colliculus. The automatic extraction of the "activated" volume using the threshold method is represented in red and the symmetric volume in green.
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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.Figure 1.3. Brain area (the superior colliculus) in which CMRGlu was significantly higher or lower in visually stimulated hemibrains than in the corresponding control hemibrains automatically detected by a voxel-wise statistical analysis. Significance is indicated with t statistic color scales, corresponding to the level of significance at voxel level.
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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 potential of the radiosensitive β-microprobe to monitor the [18F]-MPPF binding in the mouse hippocampus in vivo (Figure 1.5). Desbrée et al. IMNC, UMR8165 CNRS-University of Paris 7 and Paris 11, Orsay, France. Journal of Nuclear Medicine, 2008, 49(7):1155-61. Abstract.
Figure 1.5. 3D postmortem imaging of radioligand distribution in mouse brain after injection of [18F]-MPPF. Background black and white anatomic volumetric reconstruction of cresyl violet-stained sections shows bilateral location of 5-HT1A binding in mouse hippocampus. Pseudocolored digitized autoradiographs illustrate level of [18F]-MPPF binding and are color-coded from low (blue) to high (red) binding.
![3D postmortem imaging of radioligand distribution in mouse brain after injection of [18F]-MPPF. Background black and white anatomic volumetric reconstruction of cresyl violet-stained sections shows bilateral location of 5-HT1A binding in mouse hippocampus. Pseudocolored digitized autoradiographs illustrate level of [18F]-MPPF binding and are color-coded from low (blue) to high (red) binding.](./images/1155fig2.png)
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