June 2013

Document Type


Degree Name



Oregon Health & Science University


One of the largest subcortical structures in the mammalian brain, the thalamus transmits peripheral sensory inputs to the cortex and striatum and acts as a relay station for motor circuits. Here we describe a method for the comprehensive description of projections emanating from the thalamus, with the goal of using differences in projection patterns to suggest a structural delineation of thalamic nuclei. We used multi-color fluorescent proteins expressed in small subsets of cells in the thalamus, delivered through stereotaxic injections, in order to achieve precise and complete coverage of the volume of the thalamus. Labeled brains were then serially sectioned and imaged. Using Matlab, the image of each slice was registered through rigid body transformations into a 3- dimensional structure, and the volume of each brain was normalized to the population average. Reconstructed brain images were manually segmented into regions of interest in the striatum and cortex. Each injection was scored on the basis of its anatomical connectivity. A method to use this scoring method to parcellate thalamic nuclei is described. Maps of the long-range connectivity of groups of cells, with the mesoscopic connectome method described here, will permit the investigation of complex neural circuits underlying the activity of different brain regions.




Neuroscience Graduate Program


School of Medicine



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