An image registration pipeline for analysis of transsynaptic tracing in mice

Kwame S. Kutten, Stephen Eacker, Valina Dawson, Ted M Dawson, Tilak Ratnanather, Michael I. Miller

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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 uorescent 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 Difieomorphic 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 suficient for use with transsynaptic RbV tracing.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging
PublisherSPIE
Volume9788
ISBN (Electronic)9781510600232
DOIs
StatePublished - 2016
EventMedical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging - San Diego, United States
Duration: Mar 1 2016Mar 3 2016

Other

OtherMedical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging
CountryUnited States
CitySan Diego
Period3/1/163/3/16

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Keywords

  • LDDMM
  • Parkinson's disease
  • Registration

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Radiology Nuclear Medicine and imaging

Cite this

Kutten, K. S., Eacker, S., Dawson, V., Dawson, T. M., Ratnanather, T., & Miller, M. I. (2016). An image registration pipeline for analysis of transsynaptic tracing in mice. In Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging (Vol. 9788). [978823] SPIE. https://doi.org/10.1117/12.2216233