HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations

Abstract

We have developed new imaging and computational workflows to produce accurately aligned multimodal 3D images of the mouse brain that exploit high resolution magnetic resonance histology (MRH) and light sheet microscopy (LSM) with fully rendered 3D reference delineations of brain structures. The suite of methods starts with the acquisition of geometrically accurate (in-skull) brain MRIs using multi-gradient echo (MGRE) and new diffusion tensor imaging (DTI) at an isotropic spatial resolution of 15 um. Whole brain connectomes are generated using over 100 diffusion weighted images acquired with gradients at uniformly spaced angles. Track density images are generated at a super-resolution of 5 um. Brains are dissected from the cranium, cleared with SHIELD, stained by immunohistochemistry, and imaged by LSM at 1.8 um/pixel. LSM channels are registered into the reference MRH space along with the Allen Brain Atlas (ABA) Common Coordinate Framework version 3 (CCFv3). The result is a high-dimensional integrated volume with registration (HiDiver) that has a global alignment accuracy of 10-50 um. HiDiver enables 3D quantitative and global analyses of cells, circuits, connectomes, and CNS regions of interest (ROIs). Throughput is sufficiently high that HiDiver is now being used in comprehensive quantitative studies of the impact of gene variants and aging on rodent brain cytoarchitecture.

Restoring morphology of light sheet microscopy data based on magnetic resonance histology

“…the CCF v3 3D template constructed from a population of 1675 young adult B6 brains using autoF (Wang et al 2020). We have created an MRH atlas with a subset of these labels using specimens 200302 (male) and 200316 (female) (Johnson et al 2022). In Figure 5, we used this MRH atlas to estimate the roegional volume changes in the LSM images from tissue swelling in specimen 190108.…”

“…We have created a reduced set of labels (rCCFv3) by combining some smaller structures into a single label since mapping the smaller structures is more highly variable. A summary of those labels can be found in (Johnson et al 2022). The magnitude and variability are significant.…”

“…The acquisition was accelerated using compressed sensing(Johnson et al 2019; Wang, Cofer, et al 2018). Diffusion tensor images were acquired using a protocol described in detail in (Johnson et al 2022). The protocol employed a Stesjkal Tanner spin echo sequence with b values of 3000 s/mm 2 , 108 angular samples spaced uniformly on the unit sphere, a compression factor of 8 x yielding a large (252 GB) 4D volume with isotropic resolution of 15 μm.…”

Volumetric analysis of the aging auditory pathway using high resolution magnetic resonance histology

“…Upon aging, the mice were sacrificed, and their brains fixed, imaged, and analyzed. Johnson et al (2022) described the process of tissue preparation, imaging, analysis, and validation of accurately aligned multimodal 3D images of the mouse brain with the high-dimensional integrated volume with registration (HiDiver) suite of methods ( Johnson et al, 2022 ). This is summarized in the following sections “Tissue preparation” and “Image acquisition and analysis.” For each mouse undergoing the imaging protocol, sex, age in days, and body weight in grams were also obtained.…”

“…In recent years, advances in technology have allowed systematic analysis of mouse central brain structures by structural and functional MRI ( Wang et al, 2020 ). Johnson et al (2022) have developed a process to efficiently generate magnetic resonance histology (MRH) images of the mouse brain with comprehensive 3D volumetric labeling ( Johnson et al, 2022 ). Their results proved generalizable to different ages, sexes, and genotypes with spatial resolution more than 500,000 times that of comparable clinical protocols.…”