A brief update on physical and optical disector applications and sectioning-staining methods in neuroscience

Yurt, Kıymet Kübra; Kıvrak, Elfide Gizem; Altun, Gamze; Ali, Fathelrahman; Gasmalla, Hosam Eldeen Elsadig; Kaplan, Süleyman

doi:10.1016/j.jchemneu.2018.02.009

Cited by 16 publications

(3 citation statements)

References 97 publications

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“…Finally, we perform a control test on the different staining types-Nissl and NeuN-using the macaque 1 data. The staining methods differ in their treatment of glia: NeuN tends to label neuronal cell bodies only while Nissl indiscriminately labels both neurons and glia (Yurt et al, 2018). We show that regardless of staining type the cell densities pass the lognormality test (Figure 1 Taken together, the normality test, the quantile plots, the pairwise tests, the cell type comparison, and the staining method comparison provide compelling evidence that the logarithmized neuron densities are normally distributed across cytoarchitectonic areas.…”

Section: Lognormal Distribution Of Neurons Across Cortical Areasmentioning

confidence: 68%

“…Finally, we perform a control test on the different staining types—Nissl and NeuN—using the macaque 1 data. The staining methods differ in their treatment of glia: NeuN tends to label neuronal cell bodies only while Nissl indiscriminately labels both neurons and glia ( Yurt et al, 2018 ). We show that regardless of staining type the cell densities pass the lognormality test ( Figure 1-Figure supplement 3 ; SW test on ln( ρ ) with p > 0.05), suggesting that counting some glia in the cell densities does not confound our analysis of the macaque 1 data.…”

Section: Resultsmentioning

confidence: 99%

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Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex

Morales-Gregorio

Meegen

Albada

2022

Preprint

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Numbers of neurons and their spatial variation are fundamental organizational features of the brain. Despite the large corpus of data available in the literature, the statistical distributions of neuron densities within and across brain areas remain largely uncharacterized. Here, we show that neuron densities are compatible with a lognormal distribution across cortical areas in several mammalian species. We find that this also holds true for uniformly sampled regions across cortex as well as within cortical areas. Our findings uncover a new organizational principle of cortical cytoarchitecture. The ubiquitous lognormal distribution of neuron densities adds to a long list of lognormal variables in the brain.

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Section: Lognormal Distribution Of Neurons Across Cortical Areasmentioning

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex

Morales-Gregorio

Meegen

Albada

2022

Preprint

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“…Moreover, since specific staining agents and immunohistochemistry techniques can enhance different microscopic details, the approach described here opens the door to draw new multimodal maps of the human brain 88 , in a scalable and reproducible way. With the advancement of microscopy-oriented techniques (e.g., 50 , 82 , 89 – 92 ), we believe that closing the gap with macroscopic modalities is crucial.…”

Section: Discussionmentioning

confidence: 99%

A multimodal computational pipeline for 3D histology of the human brain

Mancini

Casamitjana

Peter

et al. 2020

Sci Rep

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Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors. Motivation. One of the major challenges in the quest to understand the human brain as a complex system is characterizing its multiscale organization. From a macroscopic anatomical perspective, the brain is subdivided into distinct structures and presents well-defined landmarks, for instance its gyri and sulci. At a much finer scale, neurons are interconnected to form complex circuits. These circuits give rise to features at coarser scales, e.g., the laminar organization of the cortex 1. Although these distinct levels of organization may seem separate, they are, in fact, deeply linked and mutually influential. One clear example is given by Alzheimer's disease, which can be described by the interactions between proteinopathy at the microscale and distributed, network-level disruptions at the macroscale 2. Understanding these multi-scale mechanisms requires a multi-scale map of the brain. However, the current concept of brain mapping is closely linked to the specific tool used to construct cartographic representations, and thus to the spatial scale of the tool. As a result, the different organizational principles can only be observed in a scale-specific fashion with dedicated tools 3. Multi-scale imaging of the human brain is therefore necessarily multimodal, as different modalities are needed to study different scales. While a macroscopic anatomical picture of the brain is easily acquired non invasively or ex vivo with magnetic resonance imaging (MRI), finer characterization requires histological procedures and microscopy. Histology and MRI are highly complementary modalities: histology produces excellent contrast at the microscopic scale using dedicated stains that target different microanatomical or cytoarchitectural features, but it is a 2D modality that also inevitably introduces distortions in the tissue during blocking and sectioning. MRI does not yield microscopic resolution, but produces undistorted 3D volumes. Therefore, the combination of these two modalities offers a solution to the problem of imaging the human brain at high resolution in 3D.

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Characterizing the Neural Substrate of Reward with the Use of Specific Brain Lesions

Cromwell

2020

Neuromethods

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A brief update on physical and optical disector applications and sectioning-staining methods in neuroscience

Cited by 16 publications

References 97 publications

Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex

Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex

A multimodal computational pipeline for 3D histology of the human brain

Characterizing the Neural Substrate of Reward with the Use of Specific Brain Lesions

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