Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections

Abstract

Techniques involving three-dimensional (3D) tissue structure reconstruction and analysis provide a better understanding of changes in molecules and function. We have developed AutoCUTS-LM, an automated system that allows the latest advances in 3D tissue reconstruction and cellular analysis developments using light microscopy on various tissues, including archived tissue. The workflow in this paper involved advanced tissue sampling methods of the human cerebral cortex, an automated serial section collection system, digital tissue library, cell detection using convolution neural network, 3D cell reconstruction, and advanced analysis. Our results demonstrated the detailed structure of pyramidal cells (number, volume, diameter, sphericity and orientation) and their 3D spatial organization are arranged in a columnar structure. The pipeline of these combined techniques provides a detailed analysis of tissues and cells in biology and pathology.

Histomorphometric comparison of left and right oviduct structure from alpaca (Vicugna pacos)

“…& Kodituwakku, 1970;Marettová & Maretta, 2014;Steinhauer et al, 2004). Several techniques and methods involving 3D tissue structures reconstruction like Automatic Collector of Ultrathin Sections for Light microscopy (AutoCUTSLM) provide a better understanding of changes in function (Larsen et al, 2021). In this work, we found no differences between left versus right oviduct as Burkitt et al ( 2010) on 3D representations of the mouse oviduct.…”

“…Normally, the oviduct regions are histologically composed by three layers (serosa, muscular and mucosa) in vicuna (Apichela et al, 2006), llama (Apichela et al, 2009), camel (Accogli et al, 2014) and other mammals (Fléchon & Hunter, 1981; Hafez & Kodituwakku, 1970; Marettová & Maretta, 2014; Steinhauer et al, 2004). Several techniques and methods involving 3D tissue structures reconstruction like Automatic Collector of Ultrathin Sections for Light microscopy (AutoCUTSLM) provide a better understanding of changes in function (Larsen et al, 2021). In this work, we found no differences between left versus right oviduct as Burkitt et al (2010) on 3D representations of the mouse oviduct.…”

Three-Dimensional Spatial Analyses of Cholinergic Neuronal Distributions Across The Mouse Septum, Nucleus Basalis, Globus Pallidus, Nucleus Accumbens, and Caudate-Putamen

“…Last, measures of the clustering and regularity of cell distributions were performed by computing Ripley’s K-functions for experimental neuronal locations as well as for 1,000 simulations of random distributions. Ripley’s K-function (Baddeley et al, 2014 ; Ripley, 1977 ) provides a quantitative measure of the structure of a point pattern, and has been widely used in the analysis of point patterns in many fields including neuroanatomy (Anton-Sanchez et al, 2014 ; Jafari-Mamaghani et al, 2010 ; Jammalamadaka et al, 2013 ; Larsen et al, 2021 ; Matamales et al, 2016 ). To calculate Ripley’s K function we used in-house programs (Pointcloud, Matlab) to determine the number of neurons (K) within a given radius (r) of each other, using the formula: where V is the volume within radius r , n is the number of neurons in the population, I is the indicator function which is 1 if the distance from point (i) to point (j) is less than or equal to radius r (Ripley, 1981 ).…”

A complementary approach for neocortical cytoarchitecture inspection with cellular resolution imaging at whole brain scale

“…For an instance, the brain slices could be collected ( Larsen et al, 2021 ) after imaging for gene expression measurement by combining single-cell sequencing with laser capture microdissection ( Chen et al, 2017 ), the in situ molecule capture approach ( Chen et al, 2022 ), the in-situ sequencing ( Wang et al, 2018 ) or the in-situ hybridization ( Fang et al, 2022 ). The bottleneck for integration of these method with ours was the specimen slice collection, especially for the thin slices that were difficult to maintain the integrality.…”