Multi-modal imaging of a single mouse brain over five orders of magnitude of resolution

Abstract

Mammalian neurons operate at length scales spanning five orders of magnitude; micron-scale-diameter myelinated axons project millimeters across brain regions, ultimately forming nanometer scale synapses on individual post-synaptic neurons. Capturing these anatomical features across that breadth of scale has required imaging samples with multiple independent imaging modalities (e.g. MRI, electron microscopy, etc.). Translating between the different modalities, however, requires imaging the same brain with each. Here, we imaged the same postmortem mouse brain over five orders of spatial resolution using MRI, whole brain micron-scale synchrotron x-ray tomography, and large volume automated serial electron microscopy. Using this pipeline, we can track individual myelinated axons previously relegated to axon bundles in diffusion tensor MRI or arbitrarily trace neurons and their processes brain-wide and identify individual synapses on them. This pipeline provides both an unprecedented look across a single brain’s multi-scaled organization as well as a vehicle for studying the brain’s multi-scale pathologies.

Post mortem mapping of connectional anatomy for the validation of diffusion MRI

“…Micron-scale synchrotron x-ray computed tomography (microCT) is a non-destructive, 3D imaging technique that can provide micron resolution images of thick tissue blocks (∼1cm cubed) (Foxley et al, 2020). Here, osmium-stained tissue is rotated through a synchrotron x-ray beam, after which a high-resolution 3D volume is reconstructed from a series of 2D x-ray back-projections.…”

“…Here, osmium-stained tissue is rotated through a synchrotron x-ray beam, after which a high-resolution 3D volume is reconstructed from a series of 2D x-ray back-projections. MicroCT of neural tissue can capture complex, 3D cellular morphologies (Andersson et al, 2021), as well as detailed, long range axonal projections (Foxley et al, 2020), making it a valuable, up-and-coming tool for microstructure validation.…”

Synchrotron X‐ray micro‐CT as a validation dataset for diffusion MRI in whole mouse brain

“…Slice numbers in (B) correspond to numbered lines crossing wholebrain results in (A) using the volumetric electron microscopy imaging capabilities of our full imaging pipeline. 29 The tractography results presented in this study (Figure 5) suggest an additional benefit of large-volume microCT. With fODFs available across the whole brain, ground-truth tractography can be correlated with axon tracings and dMRI tractography at different scales in the same specimen.…”

“…These methods provide unparalleled specificity at the cost of only allowing 1 injection per dataset, which prohibits validation of whole connectomes in individual specimens. We have shown in previous work 29 the potential for direct tracing of individual axons in synchrotron microCT datasets without the need for neural tracers. This direct approach is not feasible with standard optical methods because slice cutting and mounting are associated with tissue distortions 48 that make it prohibitively challenging to reliably trace axons across slice boundaries after digital alignment.…”

“…Recent work has shown the ability to acquire micronresolution synchrotron CT (microCT) scans of the whole mouse brain and register them with both prior whole-brain dMRI and subsequent region-of-interest (ROI) electron microscopy data. 29 In this work, we present qualitative results demonstrating that this imaging pipeline can provide an alternative, complementary ground-truth dataset for dMRI validation. Synchrotron microCT addresses the limitations of optical imaging by providing isotropic, micron-level spatial resolution across whole mouse brains with no physical sectioning, allowing for future studies validating dMRI methods at the scale of local microstructural features up to long-range white matter pathways.…”