Modified Golgi-Cox method for micrometer scale sectioning of the whole mouse brain

Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level

The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.

Hippocampal Mitochondrial Abnormalities Induced the Dendritic Complexity Reduction and Cognitive Decline in a Rat Model of Spinal Cord Injury

Spinal cord injury (SCI) is a progressive neurodegenerative disease in addition to a traumatic event. Cognitive dysfunction following SCI has been widely reported in patients and animal models. However, the neuroanatomical changes affecting cognitive function after SCI, as well as the mechanisms behind these changes, have so far remained elusive. Herein, we found that SCI accelerates oxidative stress damage of hippocampal neuronal mitochondria. Then, for the first time, we presented a three-dimensional morphological atlas of rat hippocampal neurons generated using a fluorescence Micro-Optical Sectioning Tomography system, a method that accurately identifies the spatial localization of neurons and trace neurites. We showed that the number of dendritic branches and dendritic length was decreased in late stage of SCI. Western blot and transmission electron microscopy analyses also showed a decrease in synaptic communication. In addition, a battery of behavioral tests in these animals revealed hippocampal based cognitive dysfunction, which could be attributed to changes in the dendritic complexity of hippocampal neurons. Taken together, these results suggested that mitochondrial abnormalities in hippocampal neurons induced the dendritic complexity reduction and cognitive decline following SCI. Our study highlights the neuroanatomical basis and importance of mitochondria in brain degeneration following SCI, which might contribute to propose new therapeutic strategies.

Expansion-Based Clearing of Golgi-Cox-Stained Tissue for Multi-Scale Imaging

Obtaining fine neuron morphology and connections data is extraordinarily useful in understanding the brain’s functionality. Golgi staining is a widely used method for revealing neuronal morphology. However, Golgi-Cox-stained tissue is difficult to image in three dimensions and lacks cell-type specificity, limiting its use in neuronal circuit studies. Here, we describe an expansion-based method for rapidly clearing Golgi-Cox-stained tissue. The results show that 1 mm thick Golgi-Cox-stained tissue can be cleared within 6 hours with a well preserved Golgi-Cox-stained signal. At the same time, we found for the first time that the cleared Golgi-Cox-stained samples were compatible with three-dimensional (3D) immunostaining and multi-round immunostaining. By combining the Golgi-Cox staining with tissue clearing and immunostaining, Golgi-Cox-stained tissue could be used for large-volume 3D imaging, identification of cell types of Golgi-Cox-stained cells, and reconstruction of the neural circuits at dendritic spines level. More importantly, these methods could also be applied to samples from human brains, providing a tool for analyzing the neuronal circuit of the human brain.

Deep learning based neuronal soma detection and counting for Alzheimer's disease analysis

BACKGROUND AND OBJECTIVE

Alzheimer's Disease (AD) is associated with neuronal damage and decrease. Micro-Optical Sectioning Tomography (MOST) provides an approach to acquire high-resolution images for neuron analysis in the whole-brain. Application of this technique to AD mouse brain enables us to investigate neuron changes during the progression of AD pathology. However, how to deal with the huge amount of data becomes the bottleneck.

METHODS

Using MOST technology, we acquired 3D whole-brain images of six AD mice, and sampled the imaging data of four regions in each mouse brain for AD progression analysis. To count the number of neurons, we proposed a deep learning based method by detecting neuronal soma in the neuronal images. In our method, the neuronal images were first cut into small cubes, then a Convolutional Neural Network (CNN) classifier was designed to detect the neuronal soma by classifying the cubes into three categories, "soma", "fiber", and "background".

RESULTS

Compared with the manual method and currently available NeuroGPS software, our method demonstrates faster speed and higher accuracy in identifying neurons from the MOST images. By applying our method to various brain regions of 6-month-old and 12-month-old AD mice, we found that the amount of neurons in three brain regions (lateral entorhinal cortex, medial entorhinal cortex, and presubiculum) decreased slightly with the increase of age, which is consistent with the experimental results previously reported.

CONCLUSION

This paper provides a new method to automatically handle the huge amounts of data and accurately identify neuronal soma from the MOST images. It also provides the potential possibility to construct a whole-brain neuron projection to reveal the impact of AD pathology on mouse brain.

Constructing the rodent stereotaxic brain atlas: a survey

The stereotaxic brain atlas is a fundamental reference tool commonly used in the field of neuroscience. Here we provide a brief history of brain atlas development and clarify three key conceptual elements of stereotaxic brain atlasing: brain image, atlas, and stereotaxis. We also refine four technical indices for evaluating the construction of atlases: the quality of staining and labeling, the granularity of delineation, spatial resolution, and the precision of spatial location and orientation. Additionally, we discuss state-of-the-art technologies and their trends in the fields of image acquisition, stereotaxic coordinate construction, image processing, anatomical structure recognition, and publishing: the procedures of brain atlas illustration. We believe that the use of single-cell resolution and micron-level location precision will become a future trend in the study of the stereotaxic brain atlas, which will greatly benefit the development of neuroscience.

Optimized Golgi-Cox Staining Validated in the Hippocampus of Spared Nerve Injury Mouse Model

Golgi-Cox staining has been used extensively in neuroscience. Despite its unique ability to identify neuronal interconnections and neural processes, its lack of consistency and time-consuming nature reduces its appeal to researchers. Here, using a spared nerve injury (SNI) mouse model and control mice, we present a modified Golgi-Cox staining protocol that can stain mouse hippocampal neurons within 8 days. In this improved procedure, the mouse brain was fixed with 4% paraformaldehyde and then stored in a modified Golgi-Cox solution at 37 ± 2°C. The impregnation period was reduced from 5–14 days to 36–48 h. Brain slices prepared in this way could be preserved long-term at –80°C for up to 8 weeks. In addition to minimizing frequently encountered problems and reducing the time required to conduct the method, our modified protocol maintained, and even improved, the quality of traditional Golgi-Cox staining as applied to hippocampal neuronal morphology in SNI mice.

Unveiling Hg-binding protein within black deposit formed on Golgi-Cox-stained brain neuron

BACKGROUND

Golgi-Cox staining has been conventionally used for investigating neuronal development. After the brain tissue is subject to Golgi-Cox staining, black deposits are formed on the surface of the stained neurons because of mercuric sulfide, which does not show a fluorescence response under two-photon excitation. However, we unexpectedly observed fluorescence emitted by these black deposits during two-photon fluorescence measurements. Further, the in-depth of physical and chemical methods analysis revealed that the black deposits on the stained neurons are composed of Hg-binding proteins.

METHODS

We studied black deposits present in the Golgi-Cox-stained mouse brain neurons using techniques such as multiple-photon microscopy, scan electron microscopy, micro-Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy.

RESULTS

The emitted fluorescence was because of the fluorescence groups of Hg-binding protein present within the Golgi-Cox deposits on the neuronal surface.

CONCLUSIONS

The presence of Hg-binding proteins within black deposits on the surface of Golgi-Cox-stained neurons was proven for the first time. The novel interaction between the neurons and Hg²⁺ ions during Golgi-Cox staining help to understand the mechanism of Golgi-Cox staining.

Dendritic complexity change in the triple transgenic mouse model of Alzheimer's disease

Alzheimer’s disease (AD) is an irreversible, neurodegenerative disease that is characterized by memory impairment and executive dysfunction. However, the change of fine structure of neuronal morphology remains unclear in the AD model mouse. In this study, high-resolution mouse brain sectional images were scanned by Micro-Optical Sectioning Tomography (MOST) technology and reconstructed three-dimensionally to obtain the pyramidal neurons. The method of Sholl analysis was performed to analyze the neurons in the brains of 6- and 12-month-old AD mice. The results showed that dendritic complexity was not affected in the entorhinal cortex between 6-month-old mice and 12-month-old mice. The dendritic complexity had increased in the primary motor cortex and CA1 region of hippocampus of 12- month-old mice compared with 6-month-old mice. On the contrary, dendritic complexity in the prefrontal cortex was decreased significantly between 6-month-old and 12-month-old mice. To our knowledge, this is the first study to provide high-resolution brain images of triple transgenic AD mice for statistically analyzing neuronal dendrite complexity by MOST technology to reveal the morphological changes of neurons during AD progression.

Highly green fluorescent Nb2C MXene quantum dots

Here, two dimensional Nb₂C quantum dots with green fluorescence were fabricated for the first time with a quantum yield (QY) of up to 19%, the highest reported for Nb₂C dots so far with good photostability and pH stability.

Decrease of GSK-3β Activity in the Anterior Cingulate Cortex of Shank3b -/- Mice Contributes to Synaptic and Social Deficiency

Social deficiency is one of the core syndromes of autism spectrum disorders (ASD), for which the underlying developmental mechanism still remains elusive. Anterior cingulate cortex (ACC) plays a key role in integrating social information and regulating social behavior. Recent studies have indicated that synaptic dysfunction in ACC is essential for ASD social defects. In the present study, we investigated the development of synapses and the roles of glycogen synthase kinase 3β (GSK-3β), which mediates multiple synaptic signaling pathways in ACC by using Shank3b^−/− mice (a widely used ASD mouse model). Our data revealed that Shank3b mutation abolished the social induced c-Fos expression in ACC. From 4 weeks post-birth, neurons in Shank3b^−/− ACC exhibited an obvious decrease in spine density and stubby spines. The length and thickness of post-synaptic density (PSD), the expression of vesicular glutamate transporter 2 (vGlut2) and glutamate receptor 2 (GluR2), and the frequency of miniature excitatory post-synaptic currents (mEPSCs) were significantly reduced in Shank3b^−/−ACC. Interestingly, the levels of phosphorylated GSK-3β (Ser9), which inhibits the activity of GSK-3β, decreased along the same time course as the levels of GluR2 increased in ACC during development. Shank3b mutation leads to a dramatic increase of pGSK-3β (Ser9), and decrease of pPSD95 (a substrate of GSK-3β) and GluR2. Local delivery of AAV expressing constitutively active GSK-3β restored the expression of GluR2, increased the spine density and the number of mature spines. More importantly, active GSK-3β significantly promoted the social activity of Shank3b^−/− mice. These data, in together, indicate that decrease of GSK-3β activity in ACC may contribute to the synaptic and social defects of Shank3b^−/− mice. Enhancing GSK-3β activity may be utilized to treat ASD in the future.

Review of micro-optical sectioning tomography (MOST): technology and applications for whole-brain optical imaging [Invited]

Elucidating connectivity and functionality at the whole-brain level is one of the most challenging research goals in neuroscience. Various whole-brain optical imaging technologies with submicron lateral resolution have been developed to reveal the fine structures of brain-wide neural and vascular networks at the mesoscopic level. Among them, micro-optical sectioning tomography (MOST) is attracting increasing attention, as a variety of technological variations and solutions tailored toward different biological applications have been optimized. Here, we summarize the recent development of MOST technology in whole-brain imaging and anticipate future improvements.

High dose Allura Red, rather than the ADI dose, induces structural and behavioral changes in the medial prefrontal cortex of rats and taurine can protect it

Allura Red is a food color that can lead to neurotoxicity. Taurine is an organic compound that can act as a neuroprotectant. This study aimed to assess the effects of Allura Red with or without taurine consumption on rats' medial Prefrontal Cortex (mPFC). The subjects were divided into six groups as follows: distilled water, taurine (200 mg/kg/day), and low (7 mg/kg/day = acceptable daily dose), and high (70 mg/kg/day) doses of Allura Red with or without taurine consumption for six weeks. The results of novel objects recognition and eight-arm radial maze tests indicated impairment of memory in the Allura Red groups. Subsequently, their brains were analyzed using stereological methods. Both doses of Allura Red caused an increase in working and reference memory errors during the acquisition and retention phases in comparison to the distilled water group (p < 0.01). Additionally, the high dose of Allura Red led to a reduction in the volume of mPFC (35%) and its subdivisions, number of neurons (59%) and glial cells (46%), length of dendrites, and number of spines (mushroom and thin) per dendritic length in comparison to the distilled water group (p < 0.05). The low dose group only showed a reduction in the number of glial cells. However, simultaneous treatment of rats with taurine plus Allura Red prevented the above-mentioned changes. The acceptable daily dose of Allura Red could bring about impairment in spatial learning and memory as well as in the number of glial cells. On the other hand, the high dose of Allura Red could impair learning, memory, and mPFC structure. Thus, taurine could act as a neuroprotectant.

Simultaneous acquisition of neuronal morphology and cytoarchitecture in the same Golgi-stained brain

Acquiring an accurate orientation reference is a prerequisite for precisely analysing the morphological features of Golgi-stained neurons in the whole brain. However, the same reflective imaging contrast of Golgi staining for morphology and Nissl staining for cytoarchitecture leads to the failure of distinguishing soma morphology and simultaneously co-locate cytoarchitecture. Here, we developed the dual-mode micro-optical sectioning tomography (dMOST) method to simultaneously image the reflective and fluorescent signals in three dimensions. We evaluated the feasibility of real-time fluorescent counterstaining on Golgi-stained brain tissue. With our system, we acquired whole-brain data sets of physiological and pathological Golgi-stained mouse model brains with fluorescence-labelled anatomical annotation at single-neuron resolution. We also obtained the neuronal morphology of macaque monkey brain tissue using this method. The results show that real-time acquisition of the co-located cytoarchitecture reference in the same brain greatly facilitates the precise morphological analysis of Golgi-stained neurons.

Vitamin E can improve behavioral tests impairment, cell loss, and dendrite changes in rats' medial prefrontal cortex induced by acceptable daily dose of aspartame

Aspartame is an artificial sweetener used in about 6000 sugar-free products. Aspartame consumption could be associated with various neurological disorders. This study aimed to evaluate the effect of aspartame onmedial Prefrontal Cortex (mPFC) as well as neuroprotective effects of vitamin E. The rats were divided into seven groups, including distilled water, corn oil, vitamin E (100mg/kg/day), and low (acceptable daily dose) and high doses of aspartame (40 and 200mg/kg/day) respectively, with or without vitamin E consumption, for 8 weeks. Behavioral tests were recorded and the brain was prepared for stereological assessments. Novel objects test and eight-arm radial maze showed impairmentoflong- and short-termmemoriesin aspartame groups. Besides, mPFC volume, infralimbic volume, neurons number, glial cells number, dendrites length per neuron,and number of spines per dendrite length were decreased by 7-61% in the rats treated with aspartame. However, neurons' number, glial cells number, and rats' performance in eight-arm radial mazes were improved by concomitant consumption of vitamin E and aspartame. Yet, the mPFC volume and infralimbic cortex were protected only in the rats receiving the low dose of aspartame+vitamin E. On the other hand, dendrites length, spines number,and novel object recognition were not protected by treatment with vitamin E+aspartame. The acceptable daily dose or higher doses of aspartame could induce memory impairments and cortical cells loss in mPFC. However, vitamin E could ameliorate some of these changes.

Biophotonics in China

Biophotonics is a highly interdisciplinary field where physicists, chemists, biologists, physicians and engineers work together to solve the problems appearing in biology and medicine. In China, the Biophotonics discipline is often referred to as Biomedical Photonics, under the first-level disciplines Biomedical Engineering or Optical Engineering, and was initiated in the late 1990s. Over the past 20 years, biophotonics research in China expanded extraordinarily and has reached the frontiers of the world-level sciences. This white paper introduces the research groups in the biophotonics field in China, and their representative contributions.

Plastic embedding immunolabeled large-volume samples for three-dimensional high-resolution imaging

High-resolution three-dimensional biomolecule distribution information of large samples is essential to understanding their biological structure and function. Here, we proposed a method combining large sample resin embedding with iDISCO immunofluorescence staining to acquire the profile of biomolecules with high spatial resolution. We evaluated the compatibility of plastic embedding with an iDISCO staining technique and found that the fluorophores and the neuronal fine structures could be well preserved in the Lowicryl HM20 resin, and that numerous antibodies and fluorescent tracers worked well upon Lowicryl HM20 resin embedding. Further, using fluorescence Micro-Optical sectioning tomography (fMOST) technology combined with ultra-thin slicing and imaging, we were able to image the immunolabeled large-volume tissues with high resolution.

Early-stage reduction of the dendritic complexity in basolateral amygdala of a transgenic mouse model of Alzheimer's disease

Alzheimer's disease is a representative age-related neurodegenerative disease that could result in loss of memory and cognitive deficiency. However, the precise onset time of Alzheimer's disease affecting neuronal circuits and the mechanisms underlying the changes are not clearly known. To address the neuroanatomical changes during the early pathologic developing process, we acquired the neuronal morphological characterization of AD in APP/PS1 double-transgenic mice using the Micro-Optical Sectioning Tomography system. We reconstructed the neurons in 3D datasets with a resolution of 0.32 × 0.32 × 1 μm and used the Sholl method to analyze the anatomical characterization of the dendritic branches. The results showed that, similar to the progressive change in amyloid plaques, the number of dendritic branches were significantly decreased in 9-month-old mice. In addition, a distinct reduction of dendritic complexity occurred in third and fourth-order dendritic branches of 9-month-old mice, while no significant changes were identified in these parameters in 6-month-old mice. At the branch-level, the density distribution of dendritic arbors in the radial direction decreased in the range of 40-90 μm from the neuron soma in 6-month-old mice. These changes in the dendritic complexity suggest that these reductions contribute to the progressive cognitive impairment seen in APP/PS1 mice. This work may yield insights into the early changes in dendritic abnormality and its relevance to dysfunctional mechanisms of learning, memory and emotion in Alzheimer's disease.

Optimising Golgi-Cox staining for use with perfusion-fixed brain tissue validated in the zQ175 mouse model of Huntington's disease

BACKGROUND

The Golgi-Cox stain is an established method for characterising neuron cell morphology. The method highlights neurite processes of stained cells allowing the complexity of dendritic branching to be measured.

NEW METHODS

Conventional rapid Golgi and Golgi-Cox methods all require fresh impregnation in unfixed brain blocks. Here, we describe a modified method that gives high quality staining on brain tissue blocks perfusion-fixed with 4% paraformaldehyde (PFA) and post-fixed by immersion for 24h.

RESULTS

Tissue perfused with 4% PFA and post fixed for 24h remained viable for the modified Golgi-Cox silver impregnation staining of mouse striatum from perfused wild type and zQ175. It was not found necessary to impregnate tissue blocks with Golgi solutions prior to sectioning, as post-sectioned tissues yielded equally good impregnation. Impregnation for 14 days resulted in optimal visualisation of striatal neuron and dendritic morphology. Although no modifications applied to the rapid Golgi method were reliable, the modified Golgi-Cox method yielded consistently reliable high-quality staining.

COMPARISON WITH EXISTING METHODS

The current method used fixed tissues to reduce damage and preserve cell morphology. The revised method was found to be fast, reliable and cost effective without the need for expensive staining kits and could be performed in any neuroscience lab with limited specialist equipment.

CONCLUSIONS

The present study introduces a robust reproducible and inexpensive staining method for identifying neuronal morphological changes in the post fixed mouse brain, and is suitable for assessing changes in cell morphology in models of neurodegeneration and in response to experimental treatment.

Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model

Brain surface profile is essential for brain studies, including registration, segmentation of brain structure and drawing neuronal circuits. Recent advances in high-throughput imaging techniques enable imaging whole mouse brain at micron spatial resolution and provide a basis for more fine quantitative studies in neuroscience. However, reconstructing micron resolution brain surface from newly produced neuronal dataset still faces challenges. Most current methods apply global analysis, which are neither applicable to a large imaging dataset nor to a brain surface with an inhomogeneous signal intensity. Here, we proposed a resampling-based variational model for this purpose. In this model, the movement directions of the initial boundary elements are fixed, the final positions of the initial boundary elements that form the brain surface are determined by the local signal intensity. These features assure an effective reconstruction of the brain surface from a new brain dataset. Compared with conventional typical methods, such as level set based method and active contour method, our method significantly increases the recall and precision rates above 97% and is approximately hundreds-fold faster. We demonstrated a fast reconstruction at micron level of the whole brain surface from a large dataset of hundreds of GB in size within 6 hours.

Visible rodent brain-wide networks at single-neuron resolution

There are some unsolvable fundamental questions, such as cell type classification, neural circuit tracing and neurovascular coupling, though great progresses are being made in neuroscience. Because of the structural features of neurons and neural circuits, the solution of these questions needs us to break through the current technology of neuroanatomy for acquiring the exactly fine morphology of neuron and vessels and tracing long-distant circuit at axonal resolution in the whole brain of mammals. Combined with fast-developing labeling techniques, efficient whole-brain optical imaging technology emerging at the right moment presents a huge potential in the structure and function research of specific-function neuron and neural circuit. In this review, we summarize brain-wide optical tomography techniques, review the progress on visible brain neuronal/vascular networks benefit from these novel techniques, and prospect the future technical development.

Fluorescence imaging of dendritic spines of Golgi-Cox-stained neurons using brightening background

We report a novel fluorescence imaging approach to imaging nonfluorescence-labeled biological tissue samples. The method was demonstrated by imaging neurons in Golgi-Cox-stained and epoxy-resin-embedded samples through the excitation of the background fluorescence of the specimens. The dark neurons stood out clearly against background fluorescence in the images, enabling the tracing of a single dendritic spine using both confocal and wide-field fluorescence microscopy. The results suggest that the reported fluorescence imaging method would provide an effective alternative solution to image nonfluorescence-labeled samples, and it allows tracing the dendritic spine structure of neurons.

Appraisal of the effect of brain impregnation duration on neuronal staining and morphology in a modified Golgi-Cox method

BACKGROUND

Golgi-Cox staining method is considered as one of the best neurohistological and fascinating staining techniques to reveal the cytoarchitecture of the brain. Requirement of longer time (more than a month), laborious section processing steps, requirement of sophisticated equipment's and costly ready to use kits limits extensive use of this technique.

NEW METHOD

The need for a modified staining technique is to overcome some of these hurdles. Here we describe a modification of Golgi-Cox staining involving reduced impregnation time (7 days), omitting tissue dehydration steps, and alterations in section processing steps. Different impregnation duration (7 days, 14 days, 1 month, 6 months and 10 months) effects on optimized staining of dorsal hippocampus and basolateral amygdala were investigated.

RESULTS

Modified Golgi-Cox staining method was found to be effective in staining rat hippocampus and amygdala. Impregnation for 7 days, 14 days and 1 month resulted in giving good results and they were comparable. However, artifacts were slightly elevated with 6 months group but not extensively. Impregnation for 10 months negatively affected the staining process.

COMPARISON WITH EXISTING METHOD(S)

Compared to existing methods the current method was found to be cost effective, fast, reliable and can be executed in labs where infrastructure is limited.

CONCLUSIONS

Current modification considerably benefitted in obtaining better results (good clarity and lesser artifact) in a short time. Longer impregnated brain sections were found to be unsuitable for morphometric evaluation due to more stain precipitation and artifact. The modified technique can be used to study cellular architecture in other brain regions.

Digital reconstruction of the cell body in dense neural circuits using a spherical-coordinated variational model

Mapping the neuronal circuits is essential to understand brain function. Recent technological advancements have made it possible to acquire the brain atlas at single cell resolution. Digital reconstruction of the neural circuits down to this level across the whole brain would significantly facilitate brain studies. However, automatic reconstruction of the dense neural connections from microscopic image still remains a challenge. Here we developed a spherical-coordinate based variational model to reconstruct the shape of the cell body i.e. soma, as one of the procedures for this purpose. When intuitively processing the volumetric images in the spherical coordinate system, the reconstruction of somas with variational model is no longer sensitive to the interference of the complicated neuronal morphology, and could automatically and robustly achieve accurate soma shape regardless of the dense spatial distribution, and diversity in cell size, and morphology. We believe this method would speed drawing the neural circuits and boost brain studies.

Indian-ink perfusion based method for reconstructing continuous vascular networks in whole mouse brain

The topology of the cerebral vasculature, which is the energy transport corridor of the brain, can be used to study cerebral circulatory pathways. Limited by the restrictions of the vascular markers and imaging methods, studies on cerebral vascular structure now mainly focus on either observation of the macro vessels in a whole brain or imaging of the micro vessels in a small region. Simultaneous vascular studies of arteries, veins and capillaries have not been achieved in the whole brain of mammals. Here, we have combined the improved gelatin-Indian ink vessel perfusion process with Micro-Optical Sectioning Tomography for imaging the vessel network of an entire mouse brain. With 17 days of work, an integral dataset for the entire cerebral vessels was acquired. The voxel resolution is 0.35×0.4×2.0 µm(3) for the whole brain. Besides the observations of fine and complex vascular networks in the reconstructed slices and entire brain views, a representative continuous vascular tracking has been demonstrated in the deep thalamus. This study provided an effective method for studying the entire macro and micro vascular networks of mouse brain simultaneously.

Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling

Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.

3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution

Systematic cellular and vascular configurations are essential for understanding fundamental brain anatomy and metabolism. We demonstrated a 3D brainwide cellular and vascular (called 3D BrainCV) visualization and quantitative protocol for a whole mouse brain. We developed a modified Nissl staining method that quickly labeled the cells and blood vessels simultaneously in an entire mouse brain. Terabytes 3D datasets of the whole mouse brains, with unprecedented details of both individual cells and blood vessels, including capillaries, were simultaneously imaged at 1-μm voxel resolution using micro-optical sectioning tomography (MOST). For quantitative analysis, we proposed an automatic image-processing pipeline to perform brainwide vectorization and analysis of cells and blood vessels. Six representative brain regions from the cortex to the deep, including FrA, M1, PMBSF, V1, striatum, and amygdala, and six parameters, including cell number density, vascular length density, fractional vascular volume, distance from the cells to the nearest microvessel, microvascular length density, and fractional microvascular volume, had been quantitatively analyzed. The results showed that the proximity of cells to blood vessels was linearly correlated with vascular length density, rather than the cell number density. The 3D BrainCV made overall snapshots of the detailed picture of the whole brain architecture, which could be beneficial for the state comparison of the developing and diseased brain.

Automated and accurate detection of soma location and surface morphology in large-scale 3D neuron images

Automated and accurate localization and morphometry of somas in 3D neuron images is essential for quantitative studies of neural networks in the brain. However, previous methods are limited in obtaining the location and surface morphology of somas with variable size and uneven staining in large-scale 3D neuron images. In this work, we proposed a method for automated soma locating in large-scale 3D neuron images that contain relatively sparse soma distributions. This method involves three steps: (i) deblocking the image with overlap between adjacent sub-stacks; (ii) locating the somas in each small sub-stack using multi-scale morphological close and adaptive thresholds; and (iii) fusion of the repeatedly located somas in all sub-stacks. We also describe a new method for the accurate detection of the surface morphology of somas containing hollowness; this was achieved by improving the classical Rayburst Sampling with a new gradient-based criteria. Three 3D neuron image stacks of different sizes were used to quantitatively validate our methods. For the soma localization algorithm, the average recall and precision were greater than 93% and 96%, respectively. For the soma surface detection algorithm, the overlap of the volumes created by automatic detection of soma surfaces and manually segmenting soma volumes was more than 84% for 89% of all correctly detected somas. Our method for locating somas can reveal the soma distributions in large-scale neural networks more efficiently. The method for soma surface detection will serve as a valuable tool for systematic studies of neuron types based on neuron structure.

Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues

Fluorescent proteins serve as important biomarkers for visualizing both subcellular organelles in living cells and structural and functional details in large-volume tissues or organs. However, current techniques for plastic embedding are limited in their ability to preserve fluorescence while remaining suitable for micro-optical sectioning tomography of large-volume samples. In this study, we quantitatively evaluated the fluorescence preservation and penetration time of several commonly used resins in a Thy1-eYFP-H transgenic whole mouse brain, including glycol methacrylate (GMA), LR White, hydroxypropyl methacrylate (HPMA) and Unicryl. We found that HMPA embedding doubled the eYFP fluorescence intensity but required long durations of incubation for whole brain penetration. GMA, Unicryl and LR White each penetrated the brain rapidly but also led to variable quenching of eYFP fluorescence. Among the fast-penetrating resins, GMA preserved fluorescence better than LR White and Unicryl. We found that we could optimize the GMA formulation by reducing the polymerization temperature, removing 4-methoxyphenol and adjusting the pH of the resin solution to be alkaline. By optimizing the GMA formulation, we increased percentage of eYFP fluorescence preservation in GMA-embedded brains nearly two-fold. These results suggest that modified GMA is suitable for embedding large-volume tissues such as whole mouse brain and provide a novel approach for visualizing brain-wide networks.

Quantitative study on the hygroscopic expansion of spurr resin to obtain a high-resolution atlas of the mouse brain

Ultra-thin section-based microscopic imaging is considered one of the most realistic techniques for determining fine architectures of a brain-wide neural network. In this kind of method, the sample is usually embedded in resin and then immersed in water for sectioning and imaging. The effect of resin hygroscopic expansion on data accuracy and integrity is important as it may lead to inconsistent image qualities or degeneration of sectioning properties. But few studies have been conducted on this issue. Here, we have used surface profile measurements combined with sectioning and imaging by micro-optical sectioning tomography (MOST) to quantitatively study the sectioned surface expansion of spurr resin blocks as a result of water immersion for a short time period. The expansion effect on MOST imaging is also presented. The results revealed significant differences in the surface expansion of pure resin blocks with different immersion time durations (P < 0.001). During an eight-minute immersion, the surface expansion of the experimental specimens exhibited an approximately linear increase with immersion duration, while MOST images suffered a correlated decrease in brightness. Expansion was restricted to the submicron level with immersion duration of four minutes or less, and the mean and standard deviation of the expansion measurements both reached a maximum at eight minutes. When the immersion duration exceeded eight minutes, the expansion value decreased, which was most likely related to the degeneration of mechanical properties of the resin material on the block surface. This study indicates that it is necessary to select a specific sectioning mode according to the hygroscopic expansion properties of resin materials for maintaining the accuracy and integrity of whole brain atlas data.