BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging. (9/87)

The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.  (+info)

An integrated software suite for surface-based analyses of cerebral cortex. (10/87)

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.  (+info)

Perceptions of science. The anatomical mission to Burma. (11/87)

Until the 1830s, most Americans were unfamiliar with the images of anatomy. Then a small vanguard of reformers and missionaries began to preach, at home and around the world, that an identification with the images and concepts of anatomy was a crucial part of the civilizing process. In his essay, Sappol charts the changes in the perception of self that resulted from this anatomical evangelism. Today, as anatomical images abound in the arts and the media, we still believe that anatomical images show us our inner reality.  (+info)

Gunther von Hagens and Body Worlds Part 1: the anatomist as prosektor and proplastiker. (12/87)

Recent calls to reintegrate the sciences and humanities are challenged by the contemporary work of anatomist Gunther von Hagens and his Body Worlds exhibits of plastinated cadavers. The anatomical quest to understand our physical interior has long been in tension both with aesthetic ideals and religious sensitivities regarding the metaphysical significance of the human body. Part I of this two-part Historical Note examines tensions epitomized by Goethe's figures of the prosektor and proplastiker. The former, driven by scientific curiosity, is willing to destroy, even desecrate, the human form to obtain knowledge. The latter demurs at such mutilation of our physical body, wondrous even in death--seeking instead to rejoin what the prosektor has pulled apart, to restore human dignity. In the confrontation between prosektor and proplastiker, roles disturbingly fused in the person of von Hagens himself, questions arise regarding the authenticity of models as well as the appropriate recipients of such mediated yet intimate anatomical knowledge. Part II will focus on religious perspectives on the human body, variously interpreted as God's handiwork, habitation for the soul, and vehicle of resurrection. Consideration also is given to the role of anatomist as priest, prophet, and Promethean creator, roles self-consciously embraced by von Hagens.  (+info)

A multimodal, multidimensional atlas of the C57BL/6J mouse brain. (13/87)

Strains of mice, through breeding or the disruption of normal genetic pathways, are widely used to model human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison. We have developed a digital atlas of the adult C57BL/6J mouse brain as a comprehensive framework for storing and accessing the myriad types of information about the mouse brain. Our implementation was constructed using several different imaging techniques: magnetic resonance microscopy, blockface imaging, classical histology and immunohistochemistry. Along with raw and annotated images, it contains database management systems and a set of tools for comparing information from different techniques. The framework allows facile correlation of results from different animals, investigators or laboratories by establishing a canonical representation of the mouse brain and providing the tools for the insertion of independent data into the same space as the atlas. This tool will aid in managing the increasingly complex and voluminous amounts of information about the mammalian brain. It provides a framework that encompasses genetic information in the context of anatomical imaging and holds tremendous promise for producing new insights into the relationship between genotype and phenotype. We describe a suite of tools that enables the independent entry of other types of data, facile retrieval of information and straightforward display of images. Thus, the atlas becomes a framework for managing complex genetic and epigenetic information about the mouse brain. The atlas and associated tools may be accessed at http://www.loni.ucla.edu/MAP.  (+info)

Gunther von Hagens and Body Worlds part 2: The anatomist as priest and prophet. (14/87)

Part 1 of this two-part series highlighted tensions between the anatomical quest for scientific knowledge about the human interior and artistic representations of the anatomized body, contrasting the roles of Goethe's scientific Prosektor and humanistic Proplastiker-roles disturbingly fused in Gunther von Hagens. Part 2 first examines religious interpretations of the human body that fuel the tensions manifest in anatomy art. The body in Western cultures is a sacred text amenable to interpretation as handiwork of God, habitation for the soul, and vehicle for resurrection. As handiwork of God the body beckons the anatomist's scalpel, helping establish dissection as the hallmark of Western medicine. The body as divinely designed machine encompasses the idea of an indwelling soul expressing its will in actions mediated through the intricate network of muscles-an understanding reflected in the oft occurring muscle men of early anatomical textbooks. Interconnections of body and soul in medieval somatic spirituality are examined with reference to ideas of resurrection and their impact on anatomical illustration. Part 2 concludes with consideration of von Hagens as priest and prophet, culminating in the Promethean impulse that recognizes not God but ourselves as proper owners and molders of our destiny, embodied in the plastinator's visionary quest to create the superhuman.  (+info)

Motor control in basal ganglia circuits using fMRI and brain atlas approaches. (15/87)

In this study, we examined how the motor, premotor and associative basal ganglia territories process movement parameters such as the complexity and the frequency of movement. Twelve right-handed volunteers were studied using EPI BOLD contrast (3 T) while performing audio-paced finger tapping tasks designed to differentiate basal ganglia territories. Tasks varied movement complexity (repetitive index tapping, simple sequence of finger movements and complex sequence of 10 moves) and frequency (from 0.5 to 3 Hz). Activation maps were coregistered onto a 3-D brain atlas derived from post-mortem brains. Three main patterns of activation were observed. In the posterior putamen and the sensorimotor cortex, signal increased with movement frequency but not with movement complexity. In premotor areas, the anterior putamen and the ventral posterolateral thalamus, signal increased regularly with increasing movement frequency and complexity. In rostral frontal areas, the caudate nucleus, the subthalamic nucleus and the ventral anterior/ventrolateral thalamus, signal increased mainly during the complex task and the high frequency task (3 Hz). These data show the different roles of motor, premotor and associative basal ganglia circuits in the processing of motor-related operations and suggest that activation can be precisely located within the entire circuitry of the basal ganglia.  (+info)

A digital atlas to characterize the mouse brain transcriptome. (16/87)

Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities.  (+info)