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3.  Weismann-Netter-Stuhl Syndrome:A family report 
Weismann-Netter-Stuhl (WNS) syndrome is a rare skeletal anomaly that affects the diaphyseal part of both the tibiae and fibulae with posterior cortical thickening and anteroposterior bowing. This anomaly is usually bilateral and symmetrical. The patients are generally of short stature. In some cases, a family history suggesting genetic transmission of a mutation with an unknown locus has been reported. In this paper we present an infant with WNS syndrome with bilateral involvement of the femur. Similar clinical findings were defined in three other family members.
Conflict of interest:None declared.
doi:10.4008/jcrpe.v1i4.45
PMCID: PMC3005653  PMID: 21274295
Weismann-Netter-Stuhl syndrome; femur involvement; radiography
4.  Netter's Sports Medicine 
Mayo Clinic Proceedings  2010;85(9):752-e69.
doi:10.4065/mcp.2010.0501
PMCID: PMC2931631
5.  Professor Arnold Netter 
British Medical Journal  1936;1(3925):671.
PMCID: PMC2458331
6.  Validating atlas-guided DOT: a comparison of diffuse optical tomography informed by atlas and subject-specific anatomies 
NeuroImage  2012;62(3):1999-2006.
We describe the validation of an anatomical brain atlas approach to the analysis of diffuse optical tomography (DOT). Using MRI data from 32 subjects, we compare the diffuse optical images of simulated cortical activation reconstructed using a registered atlas with those obtained using a subject’s true anatomy. The error in localization of the simulated cortical activations when using a registered atlas is due to a combination of imperfect registration, anatomical differences between atlas and subject anatomies and the localization error associated with diffuse optical image reconstruction. When using a subject-specific MRI, any localization error is due to diffuse optical image reconstruction only. In this study we determine that using a registered anatomical brain atlas results in an average localization error of approximately 18 mm in Euclidean space. The corresponding error when the subject’s own MRI is employed is 9.1 mm. In general, the cost of using atlas-guided DOT in place of subject-specific MRI-guided DOT is a doubling of the localization error. Our results show that despite this increase in error, reasonable anatomical localization is achievable even in cases where the subject-specific anatomy is unavailable.
doi:10.1016/j.neuroimage.2012.05.031
PMCID: PMC3408558  PMID: 22634215
Diffuse optical tomography; NIRS; MRI; Anatomical atlas; Registration
7.  OUT-OF-ATLAS LABELING: A MULTI-ATLAS APPROACH TO CANCER SEGMENTATION 
Conventional automated segmentation techniques for magnetic resonance imaging (MRI) fail to perform in a robust and consistent manner when brain anatomy differs wildly from expectations – as is often the case in brain cancers. We propose a novel out-of-atlas technique to estimate the spatial extent of abnormal brain regions by combining multi-atlas based segmentation with semi-local non-parametric intensity analysis. In a study with 30 clinically-acquired MRI scans of patients with malignant gliomas and 29 atlases of normal anatomy from research acquisitions, we demonstrate that this technique robustly identifies cancerous regions. The resulting segmentations could be used to study cancer morphometrics or guide selection/application/refinement of tumor analysis models or regional image quantification approaches.
doi:10.1109/ISBI.2012.6235785
PMCID: PMC3892947  PMID: 24443679
Cancer Segmentation; Tumors; Multi-Atlas Segmentation; Out-of-Atlas Labeling
8.  Anatomical Atlas-Guided Diffuse Optical Tomography of Brain Activation 
NeuroImage  2009;49(1):561-567.
We describe a neuro imaging protocol that utilizes an anatomical atlas of the human head to guide Diffuse optical tomography of human brain activation. The protocol is demonstrated by imaging the hemodynamic response to median nerve stimulation in three healthy subjects, and comparing the images obtained using a head atlas with the images obtained using the subject-specific head anatomy. The results indicate that using the head atlas anatomy it is possible to reconstruct the location of the brain activation to the expected gyrus of the brain, in agreement with the results obtained with the subject-specific head anatomy. The benefits of this novel method derive from eliminating the need for subject-specific head anatomy and thus obviating the need for a subject-specific MRI to improve the anatomical interpretation of Diffuse optical tomography images of brain activation.
doi:10.1016/j.neuroimage.2009.07.033
PMCID: PMC2858333  PMID: 19643185
Diffuse Optical Tomography; NIRS; anatomical atlas; MRI; segmentation; registration; inverse problem; human study; somatosensory; PACS: 87.19.lf; PACS: 87.19.lh
9.  Post atlantoaxial fusion for unilateral cleft of atlas posterior arch associated with os odontoideum: case report and technique note 
European Spine Journal  2011;20(Suppl 2):284-288.
A case of a 34-year-old female with unilateral cleft of atlas posterior arch associated with os odontoideum is reported. The patient had experienced neck pain for 6 months. Five days earlier to admission the pain aggravated as a result of mild head trauma from behind. Imaging examinations revealed C1–2 subluxation as well as the deformity. After 3 days of skull traction, a sound C1–2 reduction was achieved. Post atlantoaxial fusion using bilateral transarticular screws combined with C1 laminar hook on the intact side and autogenous bone graft was performed. On the sixth month of postoperative follow-up, CT revealed solid fusion was achieved. No related complications were detected within 3 years of follow-up. The clinical manifestations and imaging findings were presented. The incidence and etiopathogenesis of hypoplastic posterior arch of the atlas were concisely introduced. Techniques of post atlantoaxial fusion under circumstances of unilateral C1 posterior elements defects were discussed. The authors believe bilateral transarticular screws combined with C1 laminar hook on the intact side and autogenous bone graft can be applicable to atlantoaxial fusion on the premise of preoperative C1–2 reduction and C1 posterior arch remaining >1/2 of its full length.
doi:10.1007/s00586-011-1693-x
PMCID: PMC3111491  PMID: 21264673
Atlantoaxial fusion; Os odontoideum; Unilateral cleft of atlas posterior arch
10.  Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003 
Nucleic Acids Research  2003;31(1):272-274.
The ‘Atlas of Genetics and Cytogenetics in Oncology and Haematology’ (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in genetics. This database is made for and by researchers and clinicians, who are encouraged to contribute. The Atlas is part of the genome project and it participates in research on cancer epidemiology.
PMCID: PMC165573  PMID: 12520000
11.  Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database 
Nucleic Acids Research  2000;28(1):349-351.
The ‘Atlas of Genetics and Cytogenetics in Oncology and Haematology’ (http://www.infobiogen.fr/services/ chromcancer ) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases and genes involved in cancer. Information presented in each page is concise and updated. This database is made for and by: cytogeneticists, molecular biologists, clinicians in oncology and in haematology, and pathologists, who are encouraged to contribute.
PMCID: PMC102493  PMID: 10592271
12.  Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated 
Nucleic Acids Research  2001;29(1):303-304.
The ‘Atlas of Genetics and Cytogenetics in Oncology and Haematology’ (http://www.infobiogen.fr/services/chromcancer) is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or longer texts (deep insights), a (new) case report section, a huge portal towards genetics and/or cancer databases, and teaching items in genetics for students in medicine and the sciences. This database is made for and by clinicians and researchers in the above-mentioned fields, who are encouraged to contribute. It deals with cancer research, genomics and cytogenomics. It is at the crossroads of research, post-university teaching and telemedicine. The Atlas is available at no cost.
PMCID: PMC29834  PMID: 11125120
13.  Atlas of Salivary Gland Tumor Cytopathology, Oral & Surgical Pathology – CD-ROM Disk 2: by Kini S. & Dardick I. Pathology Images Inc, 2006 
CytoJournal  2006;3:26.
This CD-ROM version of Atlas of Salivary Gland Tumor Cytopathology, Oral & Surgical Pathology is an excellent and concise tool for easy reference during sign out of cytology and surgical cases. It is also invaluable as a teaching tool for residents and fellows.
Atlas of Salivary Gland Tumor Cytopathology, Oral & Surgical Pathology CD-ROM (ISBN 0-9736518-0-7), Published by Pathology images Inc Ottawa, Ontario K2B 7L4, Canada
doi:10.1186/1742-6413-3-26
PMCID: PMC1676013
14.  Hypertext atlas of fetal and neonatal pathology 
Diagnostic Pathology  2008;3(Suppl 1):S9.
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 . 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.
doi:10.1186/1746-1596-3-S1-S9
PMCID: PMC2500115  PMID: 18673523
15.  A digital atlas of breast histopathology: an application of web based virtual microscopy 
Journal of Clinical Pathology  2004;57(12):1288-1291.
Aims: To develop an educationally useful atlas of breast histopathology, using advanced web based virtual microscopy technology.
Methods: By using a robotic microscope and software adopted and modified from the aerial and satellite imaging industry, a virtual microscopy system was developed that allows fully automated slide scanning and image distribution via the internet. More than 150 slides were scanned at high resolution with an oil immersion ×40 objective (numerical aperture, 1.3) and archived on an image server residing in a high speed university network.
Results: A publicly available website was constructed, http://www.webmicroscope.net/breastatlas, which features a comprehensive virtual slide atlas of breast histopathology according to the World Health Organisation 2003 classification. Users can view any part of an entire specimen at any magnification within a standard web browser. The virtual slides are supplemented with concise textual descriptions, but can also be viewed without diagnostic information for self assessment of histopathology skills.
Conclusions: Using the technology described here, it is feasible to develop clinically and educationally useful virtual microscopy applications. Web based virtual microscopy will probably become widely used at all levels in pathology teaching.
doi:10.1136/jcp.2004.018739
PMCID: PMC1770524  PMID: 15563669
virtual microscopy; slide digitisation; internet; pathology; education
16.  Web-based access to an online atlas of anatomy: the Digital Anatomist Common Gateway Interface. 
A World Wide Web Common Gateway Interface package is described for accessing existing online interactive atlases of anatomy. The Web interface accesses the same 2-D and 3-D images of human neuroanatomy, knee anatomy and thoracic viscera that are currently accessed by a custom interactive atlas in distance learning courses. Although the Web interface is too slow to replace the existing atlas, it provides a parallel access path that has much broader potential for development of a distributed distance learning network in anatomy. By maintaining both access methods to the same information sources we continue to satisfy the fast interactivity needs for our local courses, while at the same time providing a migration path to the Web as the capabilities of Web browsers evolve.
Images
PMCID: PMC2579146  PMID: 8563336
17.  ATLAS-plus: Multimedia Instruction in Embryology, Gross Anatomy, and Histology 
ATLAS-plus [Advanced Tools for Learning Anatomical Structure] is a multimedia program used to assist in the teaching of anatomy at the University of Michigan Medical School. ATLAS-plus contains three courses: Histology, Embryology, and Gross Anatomy. In addition to the three courses, a glossary containing terms from the three courses is available. All three courses and the glossary are accessible in the ATLAS-plus environment. The ATLAS-plus environment provides a consistent set of tools and options so that the user can navigate easily and intelligently in and between the various courses and modules in the ATLAS-plus world. The program is a collaboration between anatomy and cell biology faculty, medical students, graphic artists, systems analysts, and instructional designers.
PMCID: PMC2248137  PMID: 1482964
18.  DigiWarp: a method for deformable mouse atlas warping to surface topographic data 
Physics in medicine and biology  2010;55(20):6197-6214.
For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L2 pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.
doi:10.1088/0031-9155/55/20/011
PMCID: PMC3051844  PMID: 20885019
19.  Atlas-Based Analysis of Neurodevelopment from Infancy to Adulthood Using Diffusion Tensor Imaging and Applications for Automated Abnormality Detection 
NeuroImage  2010;52(2):415-428.
Quantification of normal brain maturation is a crucial step in understanding developmental abnormalities in brain anatomy and function. The aim of this study was to develop atlas-based tools for time-dependent quantitative image analysis, and to characterize the anatomical changes that occur from 2 years of age to adulthood. We used large deformation diffeomorphic metric mapping to register diffusion tensor images of normal participants into the common coordinates and used a pre-segmented atlas to segment the entire brain into 176 structures. Both voxel- and atlas-based analyses reported structure that showed distinctive changes in terms of its volume and diffusivity measures. In the white matter, fractional anisotropy (FA) linearly increased with age in logarithmic scale, while diffusivity indices, such as apparent diffusion coefficient (ADC), and axial and radial diffusivity, decreased at a different rate in several regions. The average, variability, and the time course of each measured parameter are incorporated into the atlas, which can be used for automated detection of developmental abnormalities. As a demonstration of future application studies, the brainstem anatomy of cerebral palsy patients was evaluated and the altered anatomy was delineated.
doi:10.1016/j.neuroimage.2010.04.238
PMCID: PMC2886186  PMID: 20420929
20.  Robust Non-Local Multi-Atlas Segmentation of the Optic Nerve 
Proceedings of SPIE  2013;8669:86691L-.
Labeling or segmentation of structures of interest on medical images plays an essential role in both clinical and scientific understanding of the biological etiology, progression, and recurrence of pathological disorders. Here, we focus on the optic nerve, a structure that plays a critical role in many devastating pathological conditions – including glaucoma, ischemic neuropathy, optic neuritis and multiple-sclerosis. Ideally, existing fully automated procedures would result in accurate and robust segmentation of the optic nerve anatomy. However, current segmentation procedures often require manual intervention due to anatomical and imaging variability. Herein, we propose a framework for robust and fully-automated segmentation of the optic nerve anatomy. First, we provide a robust registration procedure that results in consistent registrations, despite highly varying data in terms of voxel resolution and image field-of-view. Additionally, we demonstrate the efficacy of a recently proposed non-local label fusion algorithm that accounts for small scale errors in registration correspondence. On a dataset consisting of 31 highly varying computed tomography (CT) images of the human brain, we demonstrate that the proposed framework consistently results in accurate segmentations. In particular, we show (1) that the proposed registration procedure results in robust registrations of the optic nerve anatomy, and (2) that the non-local statistical fusion algorithm significantly outperforms several of the state-of-the-art label fusion algorithms.
doi:10.1117/12.2007015
PMCID: PMC3903299  PMID: 24478826
Multi-Atlas Segmentation; Computed Tomography; Optic Nerve; Non-Local STAPLE
21.  A 3-Dimensional Atlas of Human Tongue Muscles 
The human tongue is one of the most important yet least understood structures of the body. One reason for the relative lack of research on the human tongue is its complex anatomy. This is a real barrier to investigators as there are few anatomical resources in the literature that show this complex anatomy clearly. As a result, the diagnosis and treatment of tongue disorders lags behind that for other structures of the head and neck. This report intended to fill this gap by displaying the tongue’s anatomy in multiple ways. The primary material used in this study was serial axial images of the male and female human tongue from the Visible Human (VH) Project of the National Library of Medicine. In addition, thick serial coronal sections of three human tongues were rendered translucent. The VH axial images were computer reconstructed into serial coronal sections and each tongue muscle was outlined. These outlines were used to construct a 3-dimensional computer model of the tongue that allows each muscle to be seen in its in vivo anatomical position. The thick coronal sections supplement the 3-D model by showing details of the complex interweaving of tongue muscles throughout the tongue. The graphics are perhaps the clearest guide to date to aid clinical or basic science investigators in identifying each tongue muscle in any part of the human tongue.
doi:10.1002/ar.22711
PMCID: PMC3687025  PMID: 23650264
tongue; intrinsic and extrinsic tongue muscles; neuromuscular compartments; tongue movement; speech; swallowing; respiration; 3-D reconstruction
22.  Human Brain White Matter Atlas: Identification and Assignment of Common Anatomical Structures in Superficial White Matter 
NeuroImage  2008;43(3):447-457.
Structural delineation and assignment are the fundamental steps in understanding the anatomy of the human brain. The white matter has been structurally defined in the past only at its core regions (deep white matter). However, the most peripheral white matter areas, which are interleaved between the cortex and the deep white matter, have lacked clear anatomical definitions and parcellations. We used axonal fiber alignment information from diffusion tensor imaging (DTI) to delineate the peripheral white matter, and investigated its relationship with the cortex and the deep white matter. Using DTI data from 81 healthy subjects, we identified nine common, blade-like anatomical regions, which were further parcellated into 21 subregions based on the cortical anatomy. Four short association fiber tracts connecting adjacent gyri (U-fibers) were also identified reproducibly among the healthy population. We anticipate that this atlas will be useful resource for atlas-based white matter anatomical studies.
doi:10.1016/j.neuroimage.2008.07.009
PMCID: PMC2586008  PMID: 18692144
human; white matter; atlas; association fiber; magnetic resonance imaging; diffusion tensor
23.  The Geometric Median on Riemannian Manifolds with Application to Robust Atlas Estimation 
NeuroImage  2008;45(1 Suppl):S143-S152.
One of the primary goals of computational anatomy is the statistical analysis of anatomical variability in large populations of images. The study of anatomical shape is inherently related to the construction of transformations of the underlying coordinate space, which map one anatomy to another. It is now well established that representing the geometry of shapes or images in Euclidian spaces undermines our ability to represent natural variability in populations. In our previous work we have extended classical statistical analysis techniques, such as averaging, principal components analysis, and regression, to Riemannian manifolds, which are more appropriate representations for describing anatomical variability. In this paper we extend the notion of robust estimation, a well established and powerful tool in traditional statistical analysis of Euclidian data, to manifold-valued representations of anatomical variability. In particular, we extend the geometric median, a classic robust estimator of centrality for data in Euclidean spaces. We formulate the geometric median of data on a Riemannian manifold as the minimizer of the sum of geodesic distances to the data points. We prove existence and uniqueness of the geometric median on manifolds with non-positive sectional curvature and give sufficient conditions for uniqueness on positively curved manifolds. Generalizing the Weiszfeld procedure for finding the geometric median of Euclidean data, we present an algorithm for computing the geometric median on an arbitrary manifold. We show that this algorithm converges to the unique solution when it exists. In this paper we exemplify the robustness of the estimation technique by applying the procedure to various manifolds commonly used in the analysis of medical images. Using this approach, we also present a robust brain atlas estimation technique based on the geometric median in the space of deformable images.
doi:10.1016/j.neuroimage.2008.10.052
PMCID: PMC2735114  PMID: 19056498
Robust statistics; Riemannian manifolds; Deformable Atlases; Diffeomorphisms
24.  Ideal screw entry point and projection angles for posterior lateral mass fixation of the atlas: an anatomical study 
European Spine Journal  2009;18(9):1321-1325.
Although various posterior insertion angles for screw insertion have been proposed for C1 lateral mass, substantial conclusions have not been reached regarding ideal angles and average length of the screw yet. We aimed to re-consider the morphometry and the ideal trajections of the C1 screw. Morphometric analysis was performed on 40 Turkish dried atlas vertebrae obtained from the Department of Anatomy at the Medical School of Ankara University. The quantitative anatomy of the screw entry zone, trajectories, and the ideal lengths of the screws were calculated to evaluate the feasibility of posterior screw fixation of the lateral mass of the atlas. The entry point into the lateral mass of the atlas is the intersection of the posterior arch and the C1 lateral mass. The optimum medial angle is 13.5 ± 1.9° and maximal angle of medialization is 29.4 ± 3.0°. The ideal cephalic angle is 15.2 ± 2.6°, and the maximum cephalic angle is 29.6 ± 2.6°. The optimum screw length was found to be 19.59 ± 2.20 mm. With more than 30° of medial trajections and cephalic trajections the screw penetrates into the spinal canal and atlantooccipital joint, respectively. Strikingly, in 52% of our specimens, the height of the inferior articular process was under 3.5 mm, and in 70% was under 4 mm, which increases the importance of the preparation of the screw entry site. For accommodation of screws of 3.5-mm in diameter, the starting point should be taken as the insertion of the posterior arch at the superior end of the inferior articular process with a cephalic trajection. This study may aid many surgeons in their attempts to place C1 lateral mass screws.
doi:10.1007/s00586-009-1105-7
PMCID: PMC2899538  PMID: 19644713
Atlas; C-1; Entry zone; Lateral mass screw; Morphometry; Trajection
25.  POSTURE MATCHING AND ELASTIC REGISTRATION OF A MOUSE ATLAS TO SURFACE TOPOGRAPHY RANGE DATA 
Estimation of internal mouse anatomy is required for quantitative bioluminescence or fluorescence tomography. However, only surface range data can be recovered from all-optical systems. These data are at times sparse or incomplete. We present a method for fitting an elastically deformable mouse atlas to surface topographic range data acquired by an optical system. In this method, we first match the postures of a deformable atlas and the range data of the mouse being imaged. This is achieved by aligning manually identified landmarks. We then minimize the asymmetric L2 pseudo-distance between the surface of the deformable atlas and the surface topography range data. Once this registration is accomplished, the internal anatomy of the atlas is transformed to the coordinate system of the range data using elastic energy minimization. We evaluated our method by using it to register a digital mouse atlas to a surface model produced from a manually labeled CT mouse data set. Dice coefficents indicated excellent agreement in the brain and heart, with fair agreement in the kidneys and bladder. We also present example results produced using our method to align the digital mouse atlas to surface range data.
doi:10.1109/ISBI.2009.5193060
PMCID: PMC2975998  PMID: 21072317
Deformable atlas; mouse registration; optical tomography

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