Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI

Authors:
Open Access
Publisher website
Google Scholar
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.
Funding Information
  • U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (R01-NS095985)
  • U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (R01-MH111444)
  • Howard Hughes Medical Institute
  • United States Department of Defense | Defense Advanced Research Projects Agency (W911NF-14-2-0013)
  • Stanford Neuroscience Institute, Stanford Radiology Angel Funds

This publication has 63 references indexed in Scilit: