Automatic macroscopic density artefact removal in a Nissl‐stained microscopic atlas of whole mouse brain

Ding, Wenxiang; Li, Anan; Wu, Jingpeng; Yang, Zhongqin; Meng, Yunlong; Wang, S.; Gong, Hui

doi:10.1111/jmi.12058

Cited by 35 publications

(36 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Third, axial illumination correction was performed based on the average intensity of each section. The two illumination correction steps were based on our previously developed algorithm 39 . Image preprocessing was implemented in C++ and parallel optimized using the Intel MPI Library and then executed on a computing server (72 cores, 2 GHz/core) within 6 h for each mouse brain dataset at a voxel resolution of 0.32 × 0.32 × 2 μm 3 .…”

Section: Methodsmentioning

confidence: 99%

Single-axon level morphological analysis of corticofugal projection neurons in mouse barrel field

Guo

Peng

Zhang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Corticofugal projection neurons are key components in connecting the neocortex and the subcortical regions. In the barrel field, these neurons have various projection targets and play crucial roles in the rodent whisker sensorimotor system. However, the projection features of corticofugal projection neurons at the single-axon level are far from comprehensive elucidation. Based on a brain-wide positioning system with high-resolution imaging for Thy1-GFP M-line mice brains, we reconstructed and analyzed more than one hundred corticofugal projection neurons in both layer V and VI of barrel cortex. The dual-color imaging made it possible to locate the neurons’ somata, trace their corresponding dendrites and axons and then distinguish the neurons as L5 type I/II or L6 type. The corticofugal projection pattern showed significant diversity across individual neurons. Usually, the L5 type I neurons have greater multi-region projection potential. The thalamus and the midbrain are the most frequent projection targets among the investigated multidirectional projection neurons, and the hypothalamus is particularly unique in that it only appears in multidirectional projection situations. Statistically, the average branch length of apical dendrites in multi-region projection groups is larger than that of single-region projection groups. This study demonstrated a single-axon-level analysis for barrel corticofugal projection neurons, which could provide a micro-anatomical basis for interpreting whisker sensorimotor circuit function.

show abstract

Section: Methodsmentioning

confidence: 99%

Single-axon level morphological analysis of corticofugal projection neurons in mouse barrel field

Guo

Peng

Zhang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The acquired original images were preprocessed using the customized MATLAB (MathWorks, Inc., Natick, MA, USA) software (Ding et al 2013). Briefly, owing to the nonuniform illumination, the center of the original image tiles is brighter than the marginal region with some periodic noise (Fig.…”

Section: Preprocessingmentioning

confidence: 99%

Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

Guo

Chen

et al. 2014

Cereb. Cortex

View full text Add to dashboard Cite

Jingpeng Wu and Congdi Guo contributed equally to this work.Whether vascular distribution is spatially specific among cortical columns is a fundamental yet controversial question. Here, we have obtained 1-μm resolution 3D datasets that cover the whole mouse barrel cortex by combining Nissl staining with micro-optical sectioning tomography to simultaneously visualize individual cells and blood vessels, including capillaries. Pinpointing layer IV of the posteromedial barrel subfield, direct 3D reconstruction and quantitative analysis showed that (1) penetrating vessels preferentially locate in the interbarrel septa/barrel wall (75.1%) rather than the barrel hollows, (2) the branches of 70% penetrating vessels only reach the neighboring but not always all the neighboring barrels and the other 30% extend beyond the neighboring barrels and may provide cross-barrel blood supply or drainage, (3) the branches of 59.6% penetrating vessels reach all the neighboring barrels, while the rest only reach part of them, and (4) the length density of microvessels in the interbarrel septa/barrel wall is lower than that in the barrel hollows with a ratio of 0.92. These results reveal that the penetrating vessels and microvessels exhibit a barrel-specific organization, whereas the branches of penetrating vessels do not, which suggests a much more complex vascular distribution pattern among cortical columns than previously thought.

show abstract

“…The raw data was processed by noise removal and brightness correction between adjoining slices to improve image quality [25]. Then, the voxel sizes of the Kunming and C57BL/6 datasets were resized to 0.5×0.5×0.5 µm and 0.35×0.35×0.35 µm, respectively, with cubic interpolation.…”

Section: Methodsmentioning

confidence: 99%

An Automated Three-Dimensional Detection and Segmentation Method for Touching Cells by Integrating Concave Points Clustering and Random Walker Algorithm

Meng

Gong

et al. 2014

PLoS ONE

View full text Add to dashboard Cite

Characterizing cytoarchitecture is crucial for understanding brain functions and neural diseases. In neuroanatomy, it is an important task to accurately extract cell populations' centroids and contours. Recent advances have permitted imaging at single cell resolution for an entire mouse brain using the Nissl staining method. However, it is difficult to precisely segment numerous cells, especially those cells touching each other. As presented herein, we have developed an automated three-dimensional detection and segmentation method applied to the Nissl staining data, with the following two key steps: 1) concave points clustering to determine the seed points of touching cells; and 2) random walker segmentation to obtain cell contours. Also, we have evaluated the performance of our proposed method with several mouse brain datasets, which were captured with the micro-optical sectioning tomography imaging system, and the datasets include closely touching cells. Comparing with traditional detection and segmentation methods, our approach shows promising detection accuracy and high robustness.

show abstract

Automatic macroscopic density artefact removal in a Nissl‐stained microscopic atlas of whole mouse brain

Cited by 35 publications

References 36 publications

Single-axon level morphological analysis of corticofugal projection neurons in mouse barrel field

Single-axon level morphological analysis of corticofugal projection neurons in mouse barrel field

Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

An Automated Three-Dimensional Detection and Segmentation Method for Touching Cells by Integrating Concave Points Clustering and Random Walker Algorithm

Contact Info

Product

Resources

About