Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI
Abstract
3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation within-vivobiomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Dec 03, 2019
- Source ID
- 10.1038/s41467-019-13374-0
Entities
People
- Ailey Crow
- Brian Hsueh
- Christoph Leuze
- Gary K. Steinberg
- Jennifer McNab
- Karl Deisseroth
- Li Ye
- Maged Goubran
- Markus Aswendt
- Michael M Zeineh
- Michelle Y. Cheng
- Qiyuan Tian
Organizations
- Howard Hughes Medical Institute
- National Institute of Mental Health
- National Institute of Neurological Disorders and Stroke
- United States Department of Defense