High-throughput mapping of a whole rhesus monkey brain at micrometer resolution

Abstract

Whole-brain mesoscale mapping of primates has been hindered by large brain size and the relatively low throughput of available microscopy methods. Here, we present an integrative approach that combines primate-optimized tissue sectioning and clearing with ultrahigh-speed, large-scale, volumetric fluorescence microscopy, capable of completing whole-brain imaging of a rhesus monkey at 1 µm × 1 µm × 2.5 µm voxel resolution within 100 hours. A progressive strategy is developed for high-efficiency, long-range tracing of individual axonal fibers through the dataset of hundreds of terabytes, establishing a "Serial sectioning and clearing, 3-dimensional Microscopy, with semi-Automated Reconstruction and Tracing" (SMART) pipeline. This system supports effective connectome-scale mapping of large primates that reveals distinct features of thalamocortical projections of the rhesus monkey brain at the level of individual axonal fibers.

Intravenous gene transfer throughout the brain of infant Old World primates using AAV

“…These are both key cell types implicated in neurodegenerative disorders 52,53,73,74 , and the experiments shown here open the door for comparing these cell types in diseased and healthy macaques. Moving forward, the work here will enable major efforts under the NIH BRAIN Initiative 75 , as CAP-Mac-mediated labeling can be readily combined with tissue clearing and imaging techniques to map long-range projections within the Old World primate connectome [76][77][78] . Such studies present a novel opportunity to study the macaque brain, and more generally, an opportunity to understand the inner workings of the primate CNS.…”

The cortical connectome of primate lateral prefrontal cortex

“…Another limitation of this study is that our resolution (2 mm) was not fine enough to capture the finer scaled regularities of connectivity, including columnar (Cavada and Goldman-Rakic, 1989;Schwartz and Goldman-Rakic, 1984;Selemon and Goldman-Rakic, 1988;Seltzer et al, 1996), laminar (Barbas, 2015), and layer-specific, stripe-like (Levitt et al, 1993;Lund et al, 1993) patterns observed in tracing studies. High-resolution fMRI (Huber et al, 2017;Yacoub et al, 2020) and ultrafast whole-brain fluorescence imaging (Xu et al, 2021) in primates will help better link connectivity patterns mapped by EM-fMRI and tracing in the future.…”

Tissue clearing and 3D imaging in developmental biology

“…All tissue-clearing protocols should be understood as modular toolboxes in which specific steps can be added or removed in order to adapt them to specific applications; for example, modules taken from the CUBIC and CLARITY pipelines have recently been combined to clear slices of a rhesus monkey brain (Xu et al, 2021). Most clearing protocols can be broken down to into six modules: fixation, lipid removal or delipidation, decalcification (optional), bleaching or depigmentation/decolorization (optional), labeling (optional) and optical clearing (Fig.…”