Microcomputer stereotactic atlas

A stereotactic atlas to determine thalamic target sites has been incorporated into a microcomputer. Variability studies of the thalamus with mean and standard deviations of nuclear borders are depicted graphically for overlay onto operative images. Internal landmarks traditionally used to reference target points for functional stereotaxis may be determined by conventional ventriculography or derived from magnetic resonance scans. Modeling of polyline vertices established from gray scale contour mapping and atlas reconstructions further enhance the spatial understanding of relationships to midline structures. Computer integration of anatomic reference points, graphically depicted images and stereotactic atlas data into head frame coordinates can be accomplished. This method is consistent with established stereotactic techniques and allows the visual conceptualization of imaged and graphic data for functional stereotaxis.     

Stereotactic CT scanning for the biopsy of intracranial lesions and functional neurosurgery

This report describes a system for incorporation of stereotactic CT scanning data, stereotactic arteriographic data and a computer-generated stereotactic atlas into a three-dimensional matrix utilizing an operating room computer. 86 patients have undergone computer-assisted stereotactic biopsies of intracranial lesions without mortality or neurologic morbidity. Neuroablative and neuroaugmentative procedures have been performed on 5 patients using the CT stereotactic atlas with good correlation with target points determined by ventriculography and microelectrode recording.     

A rhesus monkey reference label atlas for template driven segmentation

Background We have acquired dual‐echo spin‐echo (DE SE) MRI data of the rhesus monkey brain since 1994 as part of an ongoing study of normal aging. To analyze these legacy data for regional volume changes, we have created a reference label atlas for the Template Driven Segmentation (TDS) algorithm. Methods The atlas was manually created from DE SE legacy MRI data of one behaviorally normal, young, male rhesus monkey and consisted of 14 regions of interest (ROI’s). We analyzed the reproducibility and validity of the TDS algorithm using the atlas relative to manual segmentation. Results ROI volumes were comparable between the two segmentation methodologies, except TDS overestimated the volume of basal ganglia regions. Both methodologies were highly reproducible, but TDS had lower sensitivity and comparable specificity. Conclusions TDS segmentation calculates accurate volumes for most ROI’s. Sensitivity will be improved in future studies through the acquisition of higher quality data.     

Three-dimensional stereotactic anatomy of the human trigeminal nerve nuclear complex

The trigeminal nuclear complex and its spinal tract extend throughout the greater part of the brain-stem and at medullary levels form the target site for producing stereotactic lesions. This paper describes a method for three-dimensional drawings of this nuclear complex. A stereotactic atlas of the human brain-stem and cerebellar nuclei has formed the data base. The two-dimensional composite transverse sections, at 1-mm intervals have been digitized using an X-Y coordinate plotting microscope. Computer programs have been written to generate drawings of a single transverse hemisection as well as regeneration of the opposite hemibrain-stem section. Specific programs were used to reconstruct serial transverse section outlines and incorporate the trigeminal nuclear complex with and without hidden line removal techniques and colour graphic display facilities. Rotation about the x, y and z axes was possible and permits any view of the reconstructed specimen to be computer-generated. A further program for reconstructing structures as stereopairs is presented.     

青藏高原地区气候图解数据集

气候图解可以直观反映气象台站基本信息和气温、降水等气象数据, 是研究植被与气候关系的有效方式。为便于了解青藏高原不同植被区域气候特征, 进一步认识青藏高原植被与气候关系, 该文基于1951-1980年与1981-2010年青藏高原地区国家地面气象台站基本信息和各30年平均观测数据, 依据《中国植被》所述标准制作每个气象台站的气候图解。论文提供了青藏高原地区主要台站气候图解集, 包括两个30年时间段共计205幅图解。研究表明: (1)青藏高原地区气温和降水总体水平偏低, 前后30年年平均气温和年降水量整体呈上升趋势; (2)青藏高原地区各气象台站记录值随植被区域不同表现出较大差异。虽然青藏高原西部地区的气象台站数量很少, 但该数据集仍涵盖了高原面上的不同植被地带, 可有效运用于高原植被与气候关系研究, 为展示高原气候环境等提供便利。     

First cervical vertebra (atlas) fracture mechanism studies using finite element method.

Injury mechanisms and stress distribution patterns are important in the clinical evaluation of spinal injuries. Recognition and interpretation of the failure patterns help to determine spinal instability and consequently the choice of treatment. Although, the biomechanics responses of the atlas have received much attention, it has not been investigated using theoretical modeling. Mathematical techniques such as finite element model will provide further understanding to the injury mechanisms of the atlas, which is important for the prevention, diagnosis, and treatment of spinal injuries. In the present study, a detailed three-dimensional finite element model of the human atlas (C1) was constructed, with the geometrical data obtained using a three-dimensional digitizer. Anterior arch, superior/inferior articular processes, transverse processes, posterior arch and posterior tubercule were modeled using eight-noded brick elements. Using the material properties from literature, the 7808-finite element model was exercised under three simulated axial compressive mode of pressure loading and boundary conditions to investigate the sites of failure reported in vivo and in vitro. This report demonstrates high concentration of localized stress at the anterior and posterior archs of the atlas, which agrees well with those reported in the literature. Furthermore, under simulated hyperextension, our results agreed well with the experimental findings, which show that the groove of the posterior arch is subjected to enormous bending moment. The close agreement of the failure location provided confidence to perform further analysis and in vitro experiments. These results may be potentially used to supplement experimental research in understanding the clinical biomechanics of the atlas.     

A forebrain atlas and stereotaxic technique for the lizard,Anolis carolinensis

A forebrain atlas and stereotaxic neurosurgical techniques were developed for use in anatomical and behavioral experiments on the green anolis lizard (Anolis carolinensis). Green anoles are convenient and robust experimental subjects with a rich behavioral repertoire, the social components of which are partly under hormonal control. The technique and atlas were devised to conduct neuroethological investigations of the effect of lesions on species-typical display behavior. The atlas consists of 12 transverse sections from an average size adult male. The figures (4–15) are based on Nissl material and supplemented with fiber-stained material from adjacent sections. They appear at the end of the article. Limitations on the accuracy of stereotaxic coordinates are discussed and tables of correlative nomenclature for principal telencephalic and diencephalic nuclei are provided.     

Hypertext atlas of fetal and neonatal pathology

Hypertext atlas of fetal and neonatal pathology is a free resource for pregraduate students of medicine, pathologists and other health professionals dealing with prenatal medicine. The atlas can be found at http://www.muni.cz/atlases. The access is restricted to registered users. Concise texts summarize the gross and microscopic pathology, etiology, and clinical signs of both common and rare fetal and neonatal conditions. The texts are illustrated with over 300 images that are accompanied by short comments. The atlas offers histological pictures of high quality. Virtual microscope interface is used to access the high-resolution histological images. Fetal ultrasound video clips are included. Case studies integrate clinical history, prenatal ultrasonographic examination, gross pathology and histological features. The atlas is available in English (and Czech) and equipped with an active index. The atlas is suitable both for medical students and pathologists as a teaching and reference tool. The atlas is going to be further expanded while keeping the high quality of the images.     

A transcriptome atlas of the mouse brain at cellular resolution

A genome-wide expression atlas of the nervous system at cellular resolution would be a valuable resource for neurobiology, genetics, developmental biology and medicine. Progress in automation of in situ hybridization makes such an atlas possible. Standardized and computerized annotation of expression patterns will be critical for producing a searchable atlas database that can be accessed through the internet.     

Finessing atlas data for species distribution models

Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This study outlines the incorporation of existing knowledge into a conventional approach to predict the distribution of Bonelli’s eagle (Aquila fasciata) at a resolution 100 times finer than available atlas data. Location Malaga province, Andalusia, southern Spain. Methods A Bayesian expert system was proposed to utilize the knowledge from distribution models to yield the probability of a species being recorded at a finer resolution (1 × 1 km) than the original atlas data (10 × 10 km). The recorded probability was then used as a weight vector to generate a sampling scheme from the species atlas to enhance the accuracy of the modelling procedure. The maximum entropy for species distribution modelling (MaxEnt) was used as the species distribution model. A comparison was made between the results of the MaxEnt using the enhanced and, the random sampling scheme, based on four groups of environmental variables: topographic, climatic, biological and anthropogenic. Results The models with the sampling scheme enhanced by an expert system had a higher discriminative capacity than the baseline models. The downscaled (i.e. finer scale) species distribution maps using a hybrid MaxEnt/expert system approach were more specific to the nest locations and were more contrasted than those of the baseline model. Main conclusions The proposed method is a feasible substitute for comprehensive field work. The approach developed in this study is applicable for predicting the distribution of Bonelli’s eagle at a local scale from a national‐level occurrence data set; however, the usefulness of this approach may be limited to well‐known species.     

应用MRI预扫描定位提高大鼠脑立体定位术的准确性

目的评价MRI预扫描方法在鼠脑穿刺定位准确性上的作用与价值。材料与方法选取健康雄性SD大鼠18只,随机分为2组,分别为MRI预扫描定位组（9只）,在MR图像指导下进行穿刺注射;以及经典穿刺组（9只）,不采用MR影像学检测定位,严格按照脑立体定位图谱进行穿刺注射。穿刺以通过苍白球中心的鼠脑切面中尾状核区为靶目标,穿刺后采用MRI影像学方法确定穿刺点位置,比较MRI预扫描定位穿刺与经典立体定位穿刺的准确度。结果 MRI预扫描定位组穿刺准确率为88.89%,经典穿刺组穿刺准确率为66.67%;两种方法的穿刺定位差异有显著性（P〈0.05）,MRI预扫描组的穿刺定位准确度明显高于经典穿刺组。结论 MRI预扫描可显著提高鼠脑立体定位穿刺的准确度,是进行立体定位精细穿刺的必要操作。     

A digital three-dimensional atlas of the honeybee antennal lobe based on optical sections acquired by confocal microscopy

We present a digital atlas of the glomeruli in the antennal lobe of the honeybee, Apis mellifera, accessible to the scientific community via the Internet. The atlas allows the identification of glomeruli in preparations in which the glomeruli can be recognized, be it in sections or in whole-mounts. The high resolution of the anatomical data upon which the atlas is based and its electronic form should prove to be an important tool for anyone involved in the study of the honeybee antennal lobe. Its accessibility via the Internet is a step towards interactive and freely accessible databases of animal brains.     

A Diffusion-Tensor-Based White Matter Atlas for Rhesus Macaques

Atlases of key white matter (WM) structures in humans are widely available, and are very useful for region of interest (ROI)-based analyses of WM properties. There are histology-based atlases of cortical areas in the rhesus macaque, but none currently of specific WM structures. Since ROI-based analysis of WM pathways is also useful in studies using rhesus diffusion tensor imaging (DTI) data, we have here created an atlas based on a publicly available DTI-based template of young rhesus macaques. The atlas was constructed to mimic the structure of an existing human atlas that is widely used, making results translatable between species. Parcellations were carefully hand-drawn on a principle-direction color-coded fractional anisotropy image of the population template. The resulting atlas can be used as a reference to which registration of individual rhesus data can be performed for the purpose of white-matter parcellation. Alternatively, specific ROIs from the atlas may be warped into individual space to be used in ROI-based group analyses. This atlas will be made publicly available so that it may be used as a resource for DTI studies of rhesus macaques.     

Standardized atlas of the brain of the desert locust, Schistocerca gregaria

In order to understand the connectivity of neuronal networks, their constituent neurons should ideally be studied in a common framework. Since morphological data from physiologically characterized and stained neurons usually arise from different individual brains, this can only be performed in a virtual standardized brain that compensates for interindividual variability. The desert locust, Schistocerca gregaria, is an insect species used widely for the analysis of olfactory and visual signal processing, endocrine functions, and neural networks controlling motor output. To provide a common multi-user platform for neural circuit analysis in the brain of this species, we have generated a standardized three-dimensional brain of this locust. Serial confocal images from whole-mount locust brains were used to reconstruct 34 neuropil areas in ten brains. For standardization, we compared two different methods: an iterative shape-averaging (ISA) procedure by using affine transformations followed by iterative nonrigid registrations, and the Virtual Insect Brain (VIB) protocol by using global and local rigid transformations followed by local nonrigid transformations. Both methods generated a standard brain, but for different applications. Whereas the VIB technique was designed to visualize anatomical variability between the input brains, the purpose of the ISA method was the opposite, i.e., to remove this variability. A novel individually labeled neuron, connecting the lobula to the midbrain and deutocerebrum, has been registered into the ISA atlas and demonstrates its usefulness and accuracy for future analysis of neural networks. The locust standard brain is accessible at http://www.3d-insectbrain.com .     

The human secretome atlas initiative: Implications in health and disease conditions

Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts toward secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study. This article is part of a Special Issue entitled: An Updated Secretome.     

Stereotaxic atlas of the brain of Octodon degus.

We present a stereotaxic atlas of the brain of the trumpet-tailed rat or degu (Octodon degus), an hystricomorph rodent native to Chile and one which has become increasingly popular as a research animal, among other things because of its use as a model for diabetic cataracts and its tendency to become hyperglycemic. The atlas contains 38 transverse and two sagittal sections of the brain covering pros-, mes-, and rhombencephalon, as well as diagrams of the brain's surface anatomy. It was constructed from brains of young adult male degus but can be used readily in studies of adult females, since there is no apparent sexual dimorphism in the brain size of this rodent. Ninety percent of 40 experimental lesions used to check the accuracy of the atlas were correctly placed. The fore- and midbrain of the degu are generally more compact than corresponding regions of the brain in the laboratory rat (suborder Myomorpha) and the guinea pig (another hystricomorph). The amygdaloid complex extends further forward in the telencephalon. Major mesencephalic nuclei and fiber tracts are more rostral in position. However, superior and inferior colliculi are much longer in degus than rats. The basic organization of the rhombencephalon is similar in degus and rats, although there are clearcut differences in the length or size of some hindbrain nuclei.