Three-dimensional Local Reference Frames for Precise Neuroanatomical Modeling

Abstract

Reference frames provide a method of registering anatomical and functional data collected across multiple specimens and experimental setups into a common coordinate system in order to perform further analysis. Global reference frames define a brain-wide coordinate system and are useful when studying multiple brain regions. However, when a precise neuroanatomical model of a specific brain region is required, the precision provided by the global reference frames is insufficient and thus we require local reference frames, where the region is modeled using its local anatomical landmarks. Such a 3D local reference frame has previously been developed for the rat barrel cortex that has been applied to model its geometric, cellular and morphological organization, culminating in the generation of a dense statistical connectome of the region which predicts the connectivity between neurons of the region. I, first developed an algorithm to detect putative synaptic contacts between \emph{in vivo} labeled pairs of neurons and applied them to neuron pairs of the rat barrel cortex. The resulting number and distribution of putative synaptic contacts were in-line with the prediction of the connectome model, thus validating the model. Therefore, I extended the 3D local reference framing approach to the rat facial nucleus and applied it to obtain the organization of vibrissal motoneurons that innervate the intrinsic whisker muscles, which formed whisker row-specific slabs in the ventro-lateral facial nucleus. In order to extend the local reference framing approach to regions that lack salient anatomical features, I came up with a novel way to define a functional brain region: based on its synaptic distance from a terminal muscle. I validated the trans-synaptic spread of rabies virus using the facial nucleus reference frame, following its administration into an intrinsic whisker muscle. I defined the region spanned by rabies labeled neurons in the layer 5 of the motor cortex as vibrissal motor cortex and generated a 3D local reference frame of it. I applied the reference frame to delineate the cellular and morphological organization of the region. The precision of these 3D local reference frames - barrel cortex (±45um), facial nucleus (±60um) and vibrissal motor cortex (±70um) - were more than 6 times higher compared to the global reference frame