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29 March 2016 An image registration pipeline for analysis of transsynaptic tracing in mice
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Parkinson's Disease (PD) is a movement disorder characterized by the loss of dopamine neurons in the substantia nigra pars compacta (SNpc) and norepinephrine neurons in the locus coeruleus (LC). To further understand the pathophysiology of PD, the input neurons of the SNpc and LC will be transsynapticly traced in mice using a fluorescent recombinant rabies virus (RbV) and imaged using serial two-photon tomography (STP). A mapping between these images and a brain atlas must be found to accurately determine the locations of input neurons in the brain. Therefore a registration pipeline to align the Allen Reference Atlas (ARA) to these types of images was developed. In the preprocessing step, a brain mask was generated from the transsynaptic tracing images using simple morphological operators. The masks were then registered to the ARA using Large Deformation Diffeomorphic Metric Mapping (LDDMM), an algorithm specialized for calculating anatomically realistic transforms between images. The pipeline was then tested on an STP scan of a mouse brain labeled by an adeno-associated virus (AAV). Based on qualitative evaluation of the registration results, the pipeline was found to be sufficient for use with transsynaptic RbV tracing.
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Kwame S. Kutten, Stephen M. Eacker, Valina L. Dawson, Ted M. Dawson, Tilak Ratnanather, and Michael I. Miller "An image registration pipeline for analysis of transsynaptic tracing in mice", Proc. SPIE 9788, Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging, 978823 (29 March 2016);

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