Advances in studying whole mouse brain vasculature using high-resolution 3D light microscopy imaging

Deep learning in mesoscale brain image analysis: A review

Mesoscale microscopy images of the brain contain a wealth of information which can help us understand the working mechanisms of the brain. However, it is a challenging task to process and analyze these data because of the large size of the images, their high noise levels, the complex morphology of the brain from the cellular to the regional and anatomical levels, the inhomogeneous distribution of fluorescent labels in the cells and tissues, and imaging artifacts. Due to their impressive ability to extract relevant information from images, deep learning algorithms are widely applied to microscopy images of the brain to address these challenges and they perform superiorly in a wide range of microscopy image processing and analysis tasks. This article reviews the applications of deep learning algorithms in brain mesoscale microscopy image processing and analysis, including image synthesis, image segmentation, object detection, and neuron reconstruction and analysis. We also discuss the difficulties of each task and possible directions for further research.

epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains

During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical and pathological brain development. Here, we create high-resolution 3D atlases of the early postnatal mouse brain, using Allen CCFv3 anatomical labels, at postnatal days (P) 4, 6, 8, 10, 12, and 14, and determine the volumetric growth of different brain regions. We utilize 11 different cell type-specific transgenic animals to validate and refine anatomical labels. Moreover, we reveal region-specific density changes in γ-aminobutyric acid-producing (GABAergic), cortical layer-specific cell types, and microglia as key players in shaping early postnatal brain development. We find contrasting changes in GABAergic neuronal densities between cortical and striatal areas, stabilizing at P12. Moreover, somatostatin-expressing cortical interneurons undergo regionally distinct density reductions, while vasoactive intestinal peptide-expressing interneurons show no significant changes. Remarkably, microglia transition from high density in white matter tracks to gray matter at P10, and show selective density increases in sensory processing areas that correlate with the emergence of individual sensory modalities. Lastly, we create an open-access web-visualization ( https://kimlab.io/brain-map/epDevAtlas ) for cell-type growth charts and developmental atlases for all postnatal time points.

Vasculature in the mouse colon and spatial relationships with the enteric nervous system, glia, and immune cells

The distribution, morphology, and innervation of vasculature in different mouse colonic segments and layers, as well as spatial relationships of the vasculature with the enteric plexuses, glia, and macrophages are far from being complete. The vessels in the adult mouse colon were stained by the cardiovascular perfusion of wheat germ agglutinin (WGA)-Alexa Fluor 448 and by CD31 immunoreactivity. Nerve fibers, enteric glia, and macrophages were immunostained in the WGA-perfused colon. The blood vessels entered from the mesentery to the submucosa and branched into the capillary networks in the mucosa and muscularis externa. The capillary net formed anastomosed rings at the orifices of mucosa crypts, and the capillary rings surrounded the crypts individually in the proximal colon and more than two crypts in the distal colon. Microvessels in the muscularis externa with myenteric plexus were less dense than in the mucosa and formed loops. In the circular smooth muscle layer, microvessels were distributed in the proximal, but not the distal colon. Capillaries did not enter the enteric ganglia. There were no significant differences in microvascular volume per tissue volume between the proximal and distal colon either in the mucosa or muscularis externa containing the myenteric plexus. PGP9.5-, tyrosine hydroxylase-, and calcitonin gene-related peptide (CGRP)-immunoreactive nerve fibers were distributed along the vessels in the submucosa. In the mucosa, PGP9.5-, CGRP-, and vasoactive intestinal peptide (VIP)-immunoreactive nerves terminated close to the capillary rings, while cells and processes labeled by S100B and glial fibrillary acidic protein were distributed mainly in the lamina propria and lower portion of the mucosa. Dense Iba1 immunoreactive macrophages were closely adjacent to the mucosal capillary rings. There were a few macrophages, but no glia in apposition to microvessels in the submucosa and muscularis externa. In conclusion, in the mouse colon, (1) the differences in vasculature between the proximal and distal colon were associated with the morphology, but not the microvascular amount per tissue volume in the mucosa and muscle layers; (2) the colonic mucosa contained significantly more microvessels than the muscularis externa; and (3) there were more CGRP and VIP nerve fibers found close to microvessels in the mucosa and submucosa than in the muscle layers.

Special Section Guest Editorial: Imaging Neuroimmune, Neuroglial, and Neurovascular Interfaces

The guest editorial provides an introduction to Parts 1 and 2 of the Neurophotonics Special Section on Imaging Neuroimmune, Neuroglial, and Neurovascular Interfaces.