The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data ...sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study.
•HCP quality control procedures have enabled high throughout data acquisition.•HCP database services enable operations and open access data sharing.•Connectome Workbench enables cross-modal data visualization and exploration.
XNAT Central is a publicly accessible medical imaging data repository based on the XNAT open-source imaging informatics platform. It hosts a wide variety of research imaging data sets. The primary ...motivation for creating XNAT Central was to provide a central repository to host and provide access to a wide variety of neuroimaging data. In this capacity, XNAT Central hosts a number of data sets from research labs and investigative efforts from around the world, including the OASIS Brains imaging studies, the NUSDAST study of schizophrenia, and more. Over time, XNAT Central has expanded to include imaging data from many different fields of research, including oncology, orthopedics, cardiology, and animal studies, but continues to emphasize neuroimaging data. Through the use of XNAT's DICOM metadata extraction capabilities, XNAT Central provides a searchable repository of imaging data that can be referenced by groups, labs, or individuals working in many different areas of research. The future development of XNAT Central will be geared towards greater ease of use as a reference library of heterogeneous neuroimaging data and associated synthetic data. It will also become a tool for making data available supporting published research and academic articles.
•XNAT Central is a publicly accessible medical imaging data repository.•It runs on the widely used XNAT open-source imaging informatics platform.•It emphasizes neuroimaging data but includes imaging data from many different fields.•Research groups from around the world provide data on XNAT Central.•Future development will emphasize publishing and data management functions.
ConnectomeDB is a database for housing and disseminating data about human brain structure, function, and connectivity, along with associated behavioral and demographic data. It is the main archive ...and dissemination platform for data collected under the WU-Minn consortium Human Connectome Project. Additional connectome-style study data is and will be made available in the database under current and future projects, including the Connectome Coordination Facility. The database currently includes multiple modalities of magnetic resonance imaging (MRI) and magnetoencephalograpy (MEG) data along with associated behavioral data. MRI modalities include structural, task, resting state and diffusion. MEG modalities include resting state and task. Imaging data includes unprocessed, minimally preprocessed and analysis data. Imaging data and much of the behavioral data are publicly available, subject to acceptance of data use terms, while access to some sensitive behavioral data is restricted to qualified investigators under a more stringent set of terms. ConnectomeDB is the public side of the WU-Minn HCP database platform. As such, it is geared towards public distribution, with a web-based user interface designed to guide users to the optimal set of data for their needs and a robust backend mechanism based on the commercial Aspera fasp service to enable high speed downloads. HCP data is also available via direct shipment of hard drives and Amazon S3.
first distinguished "simple" from "complex" cells in visual cortex and proposed a processing hierarchy in which rows of LGN cells are pooled to drive oriented simple cell subunits, which are pooled ...in turn to drive complex cells. Although parsimonious and highly influential, the pure hierarchical model has since been challenged by results indicating that many complex cells receive excitatory monosynaptic input from LGN cells or do not depend on simple cell input. Alternative accounts of complex cell orientation tuning remain scant, however, and the function of monosynaptic LGN contacts onto complex cell dendrites remains unknown. We have used a biophysically detailed compartmental model to investigate whether nonlinear integration of LGN synaptic inputs within the dendrites of individual pyramidal cells could contribute to complex-cell receptive field structure. We show that an isolated cortical neuron with "active" dendrites, driven only by excitatory inputs from overlapping ON- and OFF-center LGN subfields, can produce clear phase-invariant orientation tuning-a hallmark response characteristic of a complex cell. The tuning is shown to depend critically both on the spatial arrangement of LGN synaptic contacts across the complex cell dendritic tree, established by a Hebbian developmental principle, and on the physiological efficacy of excitatory voltage-dependent dendritic ion channels. We conclude that unoriented LGN inputs to a complex cell could contribute in a significant way to its orientation tuning, acting in concert with oriented inputs to the same cell provided by simple cells or other complex cells. As such, our model provides a novel, experimentally testable hypothesis regarding the basis of orientation tuning in the complex cell population, and more generally underscores the potential importance of nonlinear intradendritic subunit processing in cortical neurophysiology.
Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and ...often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at
http://nrg.wustl.edu/software/dicom-browser
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Many complex cells in mammalian primary visual cortex are finely tuned to binocular disparity. In the prevailing model, several binocular simple cells drive each disparity-tuned complex cell. ...However, some cat complex cells receive direct LGN input, and binocular simple cells are rare in macaque. In our biophysically detailed compartmental model, active dendrites of a single neuron perform the multiple simple-cell-like subunit computations that underlie both orientation and disparity tuning. The responses of our detailed model could be predicted by a simple algebraic formula closely related to an 'energy' model. Adding inhibitory synapses led to sharper, more contrast-invariant tuning curves. Thus active dendrites could contribute to binocular-disparity tuning in complex cells.
While brain imaging in the clinical setting is largely a practice of looking at images, research neuroimaging is a quantitative and integrative enterprise. Images are run through complex batteries of ...processing and analysis routines to generate numeric measures of brain characteristics. Other measures potentially related to brain function - demographics, genetics, behavioral tests, neuropsychological tests - are key components of most research studies. The canonical scanner - PACS - viewing station axis used in clinical practice is therefore inadequate for supporting neuroimaging research. Here, we model the neuroimaging research enterprise as a workflow. The principal components of the workflow include data acquisition, data archiving, data processing and analysis, and data utilization. We also describe a set of open-source applications to support each step of the workflow and the transitions between these steps. These applications include DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE viewing and storage tools, the EXTENSIBLE NEUROIMAGING ARCHIVE TOOLKIT data archiving and exploration platform, and an engine for running processing/analysis pipelines. The overall picture presented is aimed to motivate open-source developers to identify key integration and communication points for interoperating with complimentary applications.
Microbial ecologists strive to understand the factors that influence the structures and functions of microbial communities. At first glance, understanding these communities might not seem to offer ...much to biologists studying the behaviour of animals. However, several exciting new studies demonstrate that microbial ecology has the potential to advance research on both proximate and ultimate questions in animal behaviour. Here we review three such questions: (1) how do animals recognize individuals, group members and kin, (2) how do animals choose among potential mates, and (3) what are the evolutionary costs and benefits of social relationships? Contributions to these problems from microbial ecology come from two basic ideas. First, the structure of animals’ bacterial communities is shaped by their hosts’ environments, physiologies, genotypes and social relationships. In turn, these communities can communicate this information about their animal hosts, especially through odour. Second, social relationships can mediate exposure and susceptibility to bacteria, and this socially mediated transmission can influence the evolutionary costs and benefits of social relationships. Throughout our review, we focus on the bacterial communities of vertebrates because their behaviourally relevant symbionts have received little attention compared to those of invertebrates. We focus on how new genetic tools in microbial ecology make it possible to test long-standing hypotheses in behavioural ecology, and we highlight future research directions at the interface of microbial and behavioural ecology.
In an effort to achieve a competitive advantage via cost reductions and improved market responsiveness, organisations are increasingly employing outsourcing as a major component of their supply chain ...strategies. However, as organisations increase their dependence on the suppliers of outsourced raw materials and components, they become more susceptible to their risk profiles. Supplier risk profiles are comprised of risk events which are associated with the supply network, internal operations, or external factors. Suppliers with a high probability of risk event occurrences can have a substantial impact on an organisation's revenue stream. Thus, it is essential that organisations have the means to analyse the risks associated with a supplier of outsourced materials. This article presents a methodology for analysing risks in supply networks to facilitate outsourcing decisions. The methodology includes the development of a risk profile for a given supplier through the creation of Bayesian networks. The networks are used to analyse a supplier's external, operational and network risk probabilities, and the associated revenue impact on the organisation. The methodology can be used by supply chain professionals to facilitate outsourcing decisions with either current or prospective suppliers.
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