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An atlas of forecasted molecular data. 2. Vibration frequencies of main-group and transition-metal neutral gas-phase diatomic molecules in the ground state.

This atlas of diatomic-molecular vibration frequencies parallels the previously offered Atlas of Internuclear Separations. The Atlas was produced by mining the data from Huber and Herzberg and training neural network software to forecast new data. New protocols were employed with the powerful software, which was originally designed for forecasting the financial markets. The Atlas presents 1920 additional vibration frequencies for use until critical tables are available to fill the needs more precisely. The precision of the predictions is characterized by the average fractional 1% confidence limit, that is, 10.66%. The accuracies of the predictions are determined in two ways. First, 221 of the 224 Huber and Herzberg data values used for training and validation fall within the prediction confidence limits or fall outside by less than 10% of the Huber and Herzberg values, and 181 values agree (within the limits). Second, 87 of 101 comparison data values, consisting of literature data and some additional Huber and Herzberg values, fall within the prediction confidence limits or fall outside by less than half the prediction values, and 44 of the 101 values agree (within the limits).

Journal Article↗

MRI-PET correlation in three dimensions using a volume-of-interest (VOI) atlas.

Quantitative interpretation of functional images (PET or SPECT) is hampered by poor spatial resolution, low counting statistics, and, for many tracers, low contrast between different brain structures of interest. Furthermore, normal tracer distributions can be severely disrupted by such gross pathologies as stroke, tumor, and dementia. Hence, the complementary anatomical information provided by CT or MRI is essential for accurate and reproducible regional analysis of functional data. We have developed methods for the simultaneous three-dimensional display and analysis of image volumes from MRI and PET. A general algorithm for defining the affine transformation between two equivalent point ensembles has been adapted for the purpose of registering MRI and PET image volumes by means of a simple fiducial arrangement. In addition, we have extended previous MRI-based computerized atlas methodology to three dimensions. The native atlas planes were spaced at 2 mm intervals, sufficient axial sampling to permit the generation of oblique planar sections through the atlas space. This will allow for an infinite number of angulations and axial offsets in two-dimensional region-of-interest (ROI) templates, all derived from the same master three-dimensional volume-of-interest (VOI) atlas and therefore maintaining topographical consistency throughout. These ROI templates may be selected to match the image orientation for conventional two-dimensional segmentation and data extraction.

Adult↗

Visualization, reconstruction, and integration of neuronal structures in digital brain atlases.

Brain atlases are used in neuroanatomy to define the spatial layout of neuronal structures. Their digital variant can serve as a database and common reference frame for integrating data from different biological experiments. This article presents an overview of methods for three-dimensional visualization of neuroanatomical image data, reconstructing neuronal structures from image data, creating digital brain atlases, and registering data in an atlas. This enables analysis of spatial relations between individual structures imaged in different experiments as well as between these structures and the atlas.

Animals↗

A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability.

Although there is growing interest in finding mouse models of human disease, no technique for quickly and quantitatively determining anatomical mutants currently exists. Magnetic resonance imaging (MRI) is ideally suited to probe fine structures in mice. This technology is three-dimensional, non-destructive and rapid compared to histopathology; hence MRI scientists have been able to create detailed three-dimensional images of 60 mum resolution or better. The data is digital which lends itself to sophisticated image processing algorithms. Here we show a variational MRI atlas constructed from nine excised brains of 8 week old 129S1/SvImJ male mice. This new type of atlas is comprised of an unbiased average brain--created from alignment of the individual brains--and the mathematical descriptors of anatomical variation across the individuals. We found that the majority of internal points in the individuals never varied more than 117 microm from equivalent points in the atlas. A three-dimensional annotation of the average image was performed and used to estimate the mean and standard deviation of volumes in a variety of structures across the individual brains; these volumes never differed by more than 5%. Our results indicate that variational atlases of inbred strains represent a well-defined basis against which mutant outliers can be readily compared.

Algorithms↗

Female Attacus atlas respond to pheromones of Antheraea polyphemus: a comparative electrophysiological and biochemical study.

Female Attacus atlas respond electrophysiologically to both of the Antheraea polyphemus pheromone components (E,Z)-6,11-hexadecadienyl acetate and (E,Z)-6,11-hexadecadienal. Moreover, they possess a pheromone-binding protein (PBP) and general odorant-binding proteins (GOBPs), as well as a pheromone-degrading sensillar esterase and aldehyde oxidase enzymes. They show no electroantennogram responses to their own gland extract. In contrast, female A. polyphemus do not respond to their own or to A. atlas pheromone. Male A. atlas do not detect any of the A. polyphemus compounds but only the conspecific female gland extracts. Both male A. atlas and female A. polyphemus possess PBP and GOBP but lack the pheromone-degrading esterases of male Antheraea. The results indicate that the two species use quite distinct classes of chemicals as pheromones. In spite of this, the N-terminal amino acid sequences of the PBPs show homology of 68%.

Acetates↗

A computerized system for the elastic matching of deformed radiographic images to idealized atlas images.

A system of computer programs is described which, for the first time, is able to use computerized tomographic data to automatically locate, measure, and describe anatomical structures of interest with accuracy and consistency. Input to the system consists of any digitized radiographic data. Computer assisted tomographic (CAT) scans of the head were used in this first implementation. Using these data and a predefined atlas picture representing an idealized view of the average normal image, an individualized atlas was created. From the individualized atlas, structure size, density, location displacement, and distortion may be calculated. The individualized atlas created using high resolution data, such as the CAT scan, may then be directly superimposed on pictures obtained using lower resolution modalities, such as positron emission tomographic scan images. This allows the precise location of structures poorly visualized by the secondary imaging modality. This system is capable of using either two- or three-dimensional data.

Adolescent↗

Detection and mapping of abnormal brain structure with a probabilistic atlas of cortical surfaces.

PURPOSE: We have devised, implemented, and tested a technique for creating a comprehensive probabilistic atlas of the human cerebral cortex, based on high-dimensional fluid transformations. The goal of the atlas is to detect and quantify subtle and distributed patterns of deviation from normal cortical anatomy, in a 3D brain image from any given subject. METHOD: Given a 3D MR image of a new subject, a high-resolution surface representation of the cerebral cortex is automatically extracted. The algorithm then calculates a set of high-dimensional volumetric maps, fluidly deforming this surface into structural correspondence with other cortical surfaces, selected one by one from an anatomic image database. The family of volumetric warps so constructed encodes statistical properties of local anatomical variation across the cortical surface. Additional strategies are developed to fluidly deform the sulcal patterns of different subjects into structural correspondence. A probability space of random transformations, based on the theory of anisotropic Gaussian random fields, is then used to encode information on complex variations in gyral and sulcal topography from one individual to another. A complete system of 256(2) probability density functions is computed to reflect the observed variability in stereotaxic space of the points whose correspondences are found by the warping algorithm. Confidence limits in stereotaxic space are determined for cortical surface points in the new subject's brain. RESULTS: Color-coded probability maps are generated, which highlight and quantify regional patterns of deformity in the anatomy of new subjects. These maps indicate locally the probability of each anatomic point being as unusually situated, given the distributions of corresponding points in the scans of normal subjects. 3D MRI volumes are analyzed, from subjects with clinically determined Alzheimer disease and age-matched normal subjects. CONCLUSION: Applications of the random fluid-based probabilistic atlas include the transfer of multisubject 3D functional, vascular, and histologic maps onto a single anatomic template, the mapping of 3D atlases onto the scans of new subjects, and the rapid detection, quantification, and mapping of local shape changes in 3D medical images in disease and during normal or abnormal growth and development.

Aged↗

Analyzing functional brain images in a probabilistic atlas: a validation of subvolume thresholding.

PURPOSE: The development of structural probabilistic brain atlases provides the framework for new analytic methods capable of combining anatomic information with the statistical mapping of functional brain data. Approaches for statistical mapping that utilize information about the anatomic variability and registration errors of a population within the Talairach atlas space will enhance our understanding of the interplay between human brain structure and function. METHOD: We present a subvolume thresholding (SVT) method for analyzing positron emission tomography (PET) and single photon emission CT data and determining separately the statistical significance of the effects of motor stimulation on brain perfusion. Incorporation of a priori anatomical information into the functional SVT model is achieved by selecting a proper anatomically partitioned probabilistic atlas for the data. We use a general Gaussian random field model to account for the intrinsic differences in intensity distribution across brain regions related to the physiology of brain activation, attenuation effects, dead time, and other corrections in PET imaging and data reconstruction. RESULTS: H2(15)O PET scans were acquired from six normal subjects under two different activation paradigms: left-hand and right-hand finger-tracking task with visual stimulus. Regional region-of-interest and local (voxel) group differences between the left and right motor tasks were obtained using nonparametric stochastic variance estimates. As expected from our simple finger movement paradigm, significant activation (z = 6.7) was identified in the left motor cortex for the right movement task and significant activation (z = 6.3) for the left movement task in the right motor cortex. CONCLUSION: We propose, test, and validate a probabilistic SVT method for mapping statistical variability between groups in subtraction paradigm studies of functional brain data. This method incorporates knowledge of, and controls for, anatomic variability contained in modern human brain probabilistic atlases in functional statistical mapping of the brain.

Adult↗

Atlas-based segmentation of pathological MR brain images using a model of lesion growth.

We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy.

Algorithms↗

A cross validation study of deep brain stimulation targeting: from experts to atlas-based, segmentation-based and automatic registration algorithms.

Validation of image registration algorithms is a difficult task and open-ended problem, usually application-dependent. In this paper, we focus on deep brain stimulation (DBS) targeting for the treatment of movement disorders like Parkinson's disease and essential tremor. DBS involves implantation of an electrode deep inside the brain to electrically stimulate specific areas shutting down the disease's symptoms. The subthalamic nucleus (STN) has turned out to be the optimal target for this kind of surgery. Unfortunately, the STN is in general not clearly distinguishable in common medical imaging modalities. Usual techniques to infer its location are the use of anatomical atlases and visible surrounding landmarks. Surgeons have to adjust the electrode intraoperatively using electrophysiological recordings and macrostimulation tests. We constructed a ground truth derived from specific patients whose STNs are clearly visible on magnetic resonance (MR) T2-weighted images. A patient is chosen as atlas both for the right and left sides. Then, by registering each patient with the atlas using different methods, several estimations of the STN location are obtained. Two studies are driven using our proposed validation scheme. First, a comparison between different atlas-based and nonrigid registration algorithms with a evaluation of their performance and usability to locate the STN automatically. Second, a study of which visible surrounding structures influence the STN location. The two studies are cross validated between them and against expert's variability. Using this scheme, we evaluated the expert's ability against the estimation error provided by the tested algorithms and we demonstrated that automatic STN targeting is possible and as accurate as the expert-driven techniques currently used. We also show which structures have to be taken into account to accurately estimate the STN location.

Algorithms↗

Interactive brain atlas with the Visible Human Project data: development methods and techniques.

A prototype of an interactive digital brain atlas was developed by using the Visible Human Project data set of the National Library of Medicine. This data set provides corresponding axial magnetic resonance images, computed tomographic images, and cryosections of the brain. The prototype was developed to demonstrate the techniques and methods that will be used throughout the development process of the atlas. The atlas has a graphical user interface, supports user interaction with various representations of the brain (i.e., two-dimensional and three-dimensional [3D]), and displays multiple images simultaneously. Motion sequences of the 3D brain were incorporated in the atlas to provide an important link between two-dimensional brain slices and volume-rendered 3D anatomic structures. Volume visualization tools were used to interactively render, rotate, and reslice the volumetric brain data. The brain was segmented with manual tracing, thresholding, and morphologic algorithms and then rendered with volume-rendering tools.

Anatomy, Cross-Sectional↗

A probabilistic functional atlas of the VIM nucleus constructed from pre-, intra- and postoperative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson's disease patients.

We have previously introduced a concept of a probabilistic functional atlas (PFA) to overcome limitations of the current electronic stereotactic brain atlases: anatomical nature, spatial sparseness, inconsistency and lack of population information. The PFA for the STN has already been developed. This work addresses construction of the PFA for the ventrointermediate nucleus (PFA-VIM). The PFA-VIM is constructed from pre-, intra- and postoperative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson's disease patients. The data contain the positions of the chronically implanted electrodes and their best contacts. For each patient, the intercommissural distance, height of the thalamus and width of the third ventricle were measured. An algorithm was developed to convert these data into the PFA-VIM, and to present them on axial, coronal and sagittal planes and in 3-D. The PFA-VIM gives a spatial distribution of the best contacts, and its probability is proportional to best contact concentration in a given location. The region with the highest probability corresponds to the best target. The PFA-VIM is calculated with 0.25-mm3 resolution from 107 best contacts in two situations: with and without lateral compensation against the width of the third ventricle. For the PFA-VIM compensated laterally, the anterior, lateral and dorsal coordinates of the mean value are (in mm) 6.24, 13.83, 1.68 for the left VIM and 6.54, -13.84, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts (P) are: 6.25, 14.25, 1.75, P = 16, for the left VIM, and 6.0, -14.0, 1.00, P = 18, for the right VIM. The coordinate system origin is at the posterior commissure. For the PFA-VIM not compensated laterally, the coordinates of the mean value are 6.24, 13.99, 1.68 for the left VIM and 6.53, -14.13, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts are 5.58, 13.67, 1.33, P = 14, for the left VIM, and 6.36, -14.03, 1.11, P = 17, for the right VIM. The PFA-VIM atlas overcomes several limitations of the current anatomical atlases and can improve targeting of thalamotomies and thalamic stimulations. It is dynamic and can easily be extended with new cases.

Algorithms↗

Quantification and visualization of three-dimensional inconsistency of the globus pallidus internus in the Schaltenbrand-Wahren brain atlas.

The major shortcomings of the Schaltenbrand-Wahren (SW) brain atlas include 3-dimensional (3D) inconsistency and spatial sparseness. This work quantifies and visualizes 3D inconsistency of the globus pallidus internus (GPi), a stereotactic target for the treatment of Parkinson's disease, dystonia and Huntington disease. The GPi 3D models 3D-A, 3D-C and 3D-S are reconstructed from the SW axial, coronal and sagittal microseries, respectively, by applying a shape-based (Nonuniform Rational B Splines) method. All three 3D models, placed in the SW coordinate system, are compared quantitatively in terms of location (centroids), size (volumes), shape (normalized eigen values), orientation (eigen vectors) and mutual spatial relationships (overlaps and inclusions). The analysis is done in 3D within each orientation and across them. The reconstructed 3D GPi models substantially differ in location, size and inclusion rate. The centroid of 3D-C is located more medially (15.6 mm) than those of 3D-A (17.5 mm) and 3D-S (18.2 mm), and that of 3D-A more ventrally (-2.3 mm) than those of 3D-C (-0.1 mm) and 3D-S (-0.4 mm). 3D-S has the smallest volume (347.3 mm3); 3D-A is 1.18 and 3D-C 1.85 times larger. The highest inclusion rate is for 3D-S (54.3 and 56.3%) and the lowest for 3D-C (28.8 and 30.6%). A smaller variability is observed in shape, orientation and overlap size (196.8, 196.1 and 185.5 mm3). To get a better correspondence between 3D-C and 3D-S, the coronal microseries were scaled laterally by 1.1667. This results in a substantial improvement of the inclusion rate of 3D-S (87.9%), though raising the volume mismatch to 2.16. The GPi in the SW atlas has a substantial 3D inaccuracy within each orientation and across them. Therefore, absolute and direct reliance on the original atlas is unsafe, and this atlas has to be used with great care and understanding of its limitations. As matching various SW microseries by global scaling is not feasible, we propose the target-dependent scaling based on structure centroid matching.

Brain↗

Statistical analysis of 168 bilateral subthalamic nucleus implantations by means of the probabilistic functional atlas.

OBJECTIVE: Statistical analysis of patients previously operated on may improve our methods of performing subsequent surgical procedures. In this article, we introduce a method for studying the functional properties of cerebral structures from electrophysiological and neuroimaging data by using the probabilistic functional atlas (PFA). The PFA provides a spatial distribution of the clinically most effective contacts normalized to a common space. This distribution is converted into a probability function for a given point in space to be inside an effective contact. The PFA was used to analyze spatial properties of the functional subthalamic nucleus (STN), defined as the spatial volume corresponding to the distribution of effective contacts. These results may potentially be useful in planning subthalamic implantation of electrodes. METHODS: In all, 168 bilateral subthalamic stimulations were examined. An algorithm was developed for converting these data into the PFA. The PFA for the STN (here called "atlas") was calculated with 0.25-mm3 resolution, and several features characterizing the left and right STN were studied. The analysis was performed with and without lateral compensation against the width of the third ventricle. The key feature introduced here used for analysis of the functional STN is a (probabilistic) functional volume of structure (defined for a given probability as the volume of a region whose every point has a probability equal to or greater than this given probability). RESULTS: The analysis has been performed for two situations: with and without lateral compensation against the width of the third ventricle. Without lateral compensation, the differences between the mean values and standard deviations of their barycenter coordinates for the left and right functional STNs are 0.31 and 0.18 mm, respectively. The left STN and right STN exhibit differences in functional volume size and probability distribution. The entire functional volume is 240 mm3 for the left and 229 mm3 for the right STN. A more prominent difference exists in the region of high probabilities (0.7 or higher), called "hot STN." The volume of the left hot STN is 5.52 mm3, whereas that of the right is 3.92 mm3. The left hot STN is 1.41 times bigger and 20% more dense than the right hot STN. For a given probability, the corresponding functional volume for the left hot STN is up to 43 times larger than that for the right STN. Practically speaking, lateral compensation does not change these results qualitatively. Quantitatively, differentiation between the left and right STNs is lower. For instance, for a given probability, the corresponding functional volume for the left hot STN is only up to 11 times larger than that for the right one. In either situation (i.e., with and without lateral compensation), the size of the hot STN in relation to the whole STN remains very small (1-2%). In addition, statistical analysis shows that in either situation, the means of the left and right functional STNs are significantly different. CONCLUSION: PFA-based planning may be superior to the current practice of using anatomic atlases that provide delineation of the target structure only, because it is more precise and provides a unique target point in the stereotactic space. This best stereotactic target is the point in the individualized atlas with the highest probability, meaning the highest probability of having the best target on the basis of the patients previously operated on. This best target is located in the hot STN, the size of which determines the precision of targeting. Because the size of the hot STN in comparison to the whole STN remains very small (1-2%) independent of whether or not lateral compensation is applied, target planning and execution have to be performed with high precision. The methodology presented, based on the PFA and on the functional volume, is general and can be applied to other structures and data sets. As numerous centers keep gathering large amounts of electrophysiological human and animal data, this work may facilitate opening new avenues in exploiting these data.

Brain Mapping↗

Statistical atlas of acute stroke from magnetic resonance diffusion-weighted-images of the brain.

This study presents a method for computing a probabilistic atlas that describes the spatial distributions of acute infarcts of the brain. The data consisted of diffusion-weighted-images (DWI) and high-resolution T1-weighted MR images representing 22 studies from 22 subjects. All DWI data sets contained high-intensity lesions on B-1000 maps, known from clinical history to be related to acute stroke. To compute the atlas, manually segmented infarcts on original DWI were spatially transformed and registered to a common coordinate system. This coordinate system allowed combining all lesions into a statistical atlas in the model space. As a result, the computed probabilistic map showed mild left-sided predominance of brain infarcts, which likely represents asymmetry in eloquence of brain regions. In our opinion, the statistical atlas of acute brain infarcts can facilitate computer-based detection of stroke in large image data sets.

Brain↗

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.

MOTIVATION: Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. RESULTS: We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. AVAILABILITY AND IMPLEMENTATION: The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

DNA methylation↗

Review of the Bethesda System atlas does not improve reproducibility or accuracy in the classification of atypical squamous cells of undetermined significance smears.

BACKGROUND: The Bethesda System (TBS) and its accompanying atlas were developed to promote uniform diagnosis and reporting of cervical and vaginal cytology, especially with respect to borderline abnormal smears. The authors assessed whether group study of TBS atlas improves the reproducibility and accuracy of the cytopathologic diagnosis of equivocal Papanicolaou smears. METHODS: One hundred "atypical" smears were divided into pretest and posttest sets containing equal numbers of negative, atypical squamous cells of undetermined significance (ASCUS), and squamous intraepithelial lesion (SIL) diagnoses based on a five-member panel review. Two comparable teams of four pathologists from George Washington University Medical Center (Washington, DC) and Kaiser Permanente (Portland, OR), each comprised of two more experienced cytopathologists and two less experienced pathologists, independently reviewed the 50 pretest slides and classified the slides according to TBS as negative, ASCUS, or SIL. The teams then conducted group study sessions using TBS atlas. After the review, the pathologists independently classified the 50 posttest slides in a similar manner. RESULTS: Pretest, pair-wise interobserver agreement ranged from 30% to 66% compared with 34-62% for posttest agreement. Absolute percent agreement of reviewers' diagnoses with a previously developed consensus diagnosis based on opinions of a five-expert panel (cytopathologic certainty scale) ranged from 44% to 62% for the pretest set and from 40% to 60% for the posttest set. Comparison of the detection of oncogenic human papilloma virus (HPV) DNA by hybrid capture tube test with smears classified as negative, ASCUS, or SIL revealed that seven of eight reviewers did not demonstrate a stronger association between HPV detection and cytologic diagnosis in the posttest set. CONCLUSIONS: Review of TBS atlas by itself does not appear to improve the reproducibility or accuracy of cytologic diagnoses. The lack of improvement was similar among the pathologists involved regardless of experience level or whether they had a close working relation. Cancer (Cancer Cytopathol)

Cervix Uteri↗

An anatomical atlas to support the virtual planning of hip operations.

Two three-dimensional digitized atlases of a female and a male pelvis were generated to support the virtual 3D-planning of hip operations. Beside the anatomical labeling of bone structures the determination of orthopedic measures, like angles, distances or sizes of contact areas, is important for the planning of hip operations. Thus, each atlas consists of labeled reference CT data sets, a set of landmarks as well as definitions of orthopedic measures and methods for their automatic computation. Furthermore, methods for the automatic transfer of anatomical labels from the atlas to an individual data set are presented resulting in three-dimensional models of the patient's bone structures. The anatomical atlases are designed to replace the interactive, time-consuming pre-processing steps for the virtual 3D operation planning.

Anatomy, Artistic↗