oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 15 )

2018 ( 63 )

2017 ( 60 )

2016 ( 83 )

Custom range...

Search Results: 1 - 10 of 30964 matches for " Thomas Wachtler "
All listed articles are free for downloading (OA Articles)
Page 1 /30964
Display every page Item
A distributed code for color in natural scenes derived from center-surround filtered cone signals
Christian J. Kellner,Thomas Wachtler
Frontiers in Psychology , 2013, DOI: 10.3389/fpsyg.2013.00661
Abstract: In the retina of trichromatic primates, chromatic information is encoded in an opponent fashion and transmitted to the lateral geniculate nucleus (LGN) and visual cortex via parallel pathways. Chromatic selectivities of neurons in the LGN form two separate clusters, corresponding to two classes of cone opponency. In the visual cortex, however, the chromatic selectivities are more distributed, which is in accordance with a population code for color. Previous studies of cone signals in natural scenes typically found opponent codes with chromatic selectivities corresponding to two directions in color space. Here we investigated how the non-linear spatio-chromatic filtering in the retina influences the encoding of color signals. Cone signals were derived from hyper-spectral images of natural scenes and preprocessed by center-surround filtering and rectification, resulting in parallel ON and OFF channels. Independent Component Analysis (ICA) on these signals yielded a highly sparse code with basis functions that showed spatio-chromatic selectivities. In contrast to previous analyses of linear transformations of cone signals, chromatic selectivities were not restricted to two main chromatic axes, but were more continuously distributed in color space, similar to the population code of color in the early visual cortex. Our results indicate that spatio-chromatic processing in the retina leads to a more distributed and more efficient code for natural scenes.
CoCoMac 2.0 and the future of tract-tracing databases
Rembrandt Bakker,Thomas Wachtler,Markus Diesmann
Frontiers in Neuroinformatics , 2012, DOI: 10.3389/fninf.2012.00030
Abstract: The CoCoMac database contains the results of several hundred published axonal tract-tracing studies in the macaque monkey brain. The combined results are used for constructing the macaque macro-connectome. Here we discuss the redevelopment of CoCoMac and compare it to six connectome-related projects: two online resources that provide full access to raw tracing data in rodents, a connectome viewer for advanced 3D graphics, a partial but highly detailed rat connectome, a brain data management system that generates custom connectivity matrices, and a software package that covers the complete pipeline from connectivity data to large-scale brain simulations. The second edition of CoCoMac features many enhancements over the original. For example, a search wizard is provided for full access to all tables and their nested dependencies. Connectivity matrices can be computed on demand in a user-selected nomenclature. A new data entry system is available as a preview, and is to become a generic solution for community-driven data entry in manually collated databases. We conclude with the question whether neuronal tracing will remain the gold standard to uncover the wiring of brains, thereby highlighting developments in human connectome construction, tracer substances, polarized light imaging, and serial block-face scanning electron microscopy.
A Bottom-up Approach to Data Annotation in Neurophysiology
Jan Grewe,Thomas Wachtler,Jan Benda
Frontiers in Neuroinformatics , 2011, DOI: 10.3389/fninf.2011.00016
Abstract: Metadata providing information about the stimulus, data acquisition, and experimental conditions are indispensable for the analysis and management of experimental data within a lab. However, only rarely are metadata available in a structured, comprehensive, and machine-readable form. This poses a severe problem for finding and retrieving data, both in the laboratory and on the various emerging public data bases. Here, we propose a simple format, the “open metaData Markup Language” (odML), for collecting and exchanging metadata in an automated, computer-based fashion. In odML arbitrary metadata information is stored as extended key–value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability. We started to define such terminologies for neurophysiological data, but aim at a community driven extension and refinement of the proposed definitions. By customized terminologies that map to these standard terminologies, metadata can be named and organized as required or preferred without softening the standard. Together with the respective libraries provided for common programming languages, the odML format can be integrated into the laboratory workflow, facilitating automated collection of metadata information where it becomes available. The flexibility of odML also encourages a community driven collection and definition of terms used for annotating data in the neurosciences.
Scale-invariance of receptive field properties in primary visual cortex
Tobias Teichert, Thomas Wachtler, Frank Michler, Alexander Gail, Reinhard Eckhorn
BMC Neuroscience , 2007, DOI: 10.1186/1471-2202-8-38
Abstract: We found that the sizes of both grating summation field and inhibitory surround increase with preferred spatial wavelength. For the summation field this increase, however, is not strictly linear. No evidence was found that size of the linking field depends on preferred spatial wavelength.Our data show that some receptive field properties are related to preferred spatial wavelength. This speaks in favor of the hypothesis that processing in V1 supports scale-invariant aspects of visual performance. However, not all properties of receptive fields in V1 scale with preferred spatial wavelength. Spatial-wavelength independence of the linking field implies a constant spatial range of signal coupling between neurons with different preferred spatial wavelengths. This might be important for encoding extended broad-band visual features such as edges.The primate visual system is capable of processing visual scenes at a large range of different spatial scales. Neurons with receptive fields that are scaled in size with preferred spatial wavelength1 possibly support this achievement. To investigate the potential role of primary visual cortex (V1) in this process we examined to what extent receptive field (RF) properties in V1 scale with preferred spatial wavelength. So far, systematic data for the relation of preferred wavelength and receptive field size are only available for the minimum response field (mRF) [1-6]. However, receptive fields are not described exhaustively by the mRF alone. We investigated scaling properties of several other receptive field measures.Scale invariance of psychophysical performance has been investigated for a variety of tasks. While detection thresholds of luminance defined gratings depend on scale [7], other tasks such as detection of change in spatial frequency, amplitude or orientation [8,9] of suprathreshold gratings do not depend on spatial scale. Polat and Sagi [10] examined the dependency of lateral interactions on spatial scale in a contrast d
Integrated platform and API for electrophysiological data
Andrey Sobolev,Adrian Stoewer,Aljoscha Leonhardt,Philipp L. Rautenberg,Christian J. Kellner,Christian Garbers,Thomas Wachtler
Frontiers in Neuroinformatics , 2014, DOI: 10.3389/fninf.2014.00032
Abstract: Recent advancements in technology and methodology have led to growing amounts of increasingly complex neuroscience data recorded from various species, modalities, and levels of study. The rapid data growth has made efficient data access and flexible, machine-readable data annotation a crucial requisite for neuroscientists. Clear and consistent annotation and organization of data is not only an important ingredient for reproducibility of results and re-use of data, but also essential for collaborative research and data sharing. In particular, efficient data management and interoperability requires a unified approach that integrates data and metadata and provides a common way of accessing this information. In this paper we describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API). Data representation and API structure are compatible with existing approaches for data and metadata representation in neurophysiology. The API implementation is based on the Representational State Transfer (REST) pattern, which enables data access integration in software applications and facilitates the development of tools that communicate with the service. Client libraries that interact with the API provide direct data access from computing environments like Matlab or Python, enabling integration of data management into the scientist's experimental or analysis routines.
Neo: an object model for handling electrophysiology data in multiple formats
Samuel Garcia,Domenico Guarino,Florent Jaillet,Todd Jennings,Robert Pr?pper,Philipp L. Rautenberg,Chris C. Rodgers,Andrey Sobolev,Thomas Wachtler,Pierre Yger,Andrew P. Davison
Frontiers in Neuroinformatics , 2014, DOI: 10.3389/fninf.2014.00010
Abstract: Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.
NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications
Philipp L. Rautenberg,Ajayrama Kumaraswamy,Alvaro Tejero-Cantero,Christoph Doblander,Mohammad R. Norouzian,Kazuki Kai,Hiroyuki Ai,Thomas Wachtler,Hidetoshi Ikeno
Frontiers in Neuroinformatics , 2014, DOI: 10.3389/fninf.2014.00055
Abstract: Neuroscience today deals with a “data deluge” derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing—thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations.
Humanities for medical students? A qualitative study of a medical humanities curriculum in a medical school program
Caroline Wachtler, Susanne Lundin, Margareta Troein
BMC Medical Education , 2006, DOI: 10.1186/1472-6920-6-16
Abstract: Our theoretical approach in this study is informed by derridean deconstruction and by post-structuralist analysis. We examined the ideology of the Humanities and Medicine program at Lund University, Sweden, the practical implementation of the program, and how ideology and practice corresponded. Examination of the ideology driving the humanities and medicine program was based on a critical reading of all available written material concerning the Humanities and Medicine project. The practice of the program was examined by means of a participatory observation study of one course, and by in-depth interviews with five students who participated in the course. Data was analysed using a hermeneutic editing approach.The ideological language used to describe the program calls it an interdisciplinary learning environment but at the same time shows that the conditions of the program are established by the medical faculty's agenda. In practice, the "humanities" are constructed, defined and used within a medical frame of reference. Medical students have interesting discussions, acquire concepts and enjoy the program. But they come away lacking theoretical structure to understand what they have learned. There is no place for humanities students in the program.A challenge facing cross-disciplinary programs is creating an environment where the disciplines have equal standing and contribution.Over the past 30 years there has been a trend towards the development of humanities curriculum in medical education, both in the United States and Europe. [1-3] Primarily, humanities researchers have developed the area of medical humanities, a discipline that is often part of a medical school faculty. Medical humanities can be defined as the application of the techniques of reporting, interpreting and theorising developed by the traditional humanities fields to phenomena within the traditional medical field [4].The medical humanities can have both instrumental and non-instrumental functions in a
Pain, power and patience - A narrative study of general practitioners' relations with chronic pain patients
Mia Kristiansson, Annika Brorsson, Caroline Wachtler, Margareta Troein
BMC Family Practice , 2011, DOI: 10.1186/1471-2296-12-31
Abstract: Our theoretical perspective is constructivist, based upon the relativist view that individuals construct realities to understand and navigate the world. Five Swedish General Practitioners (GPs), two male and three female, were interviewed and asked to tell a story about a difficult encounter with a chronic pain patient. Tapes of the interviews were transcribed and analysed using narrative analysis. Three GPs told narratives suited for our analytic tools and these were included in the final results.Each narrative highlights a certain dilemma and a strategy. The dilemmas were: power game; good intentions that fail when a patient is persuaded against her own conviction; persuasion of the unwilling; transferred tiredness; distrust and dissociation from the patient. Professional strategies of listening, encouraging and teamwork were central to handling difficult situations.The narratives show that GP's consultations with chronic pain patients sometimes are characterized by conflicts and difficult situations. They are facilitated by methods such as active listening and teamwork, but still may remain hard to handle. This has not before been studied among Swedish GPs. Narratives based on experience are known to be successful in education and this study suggest how narratives can serve as a training of consultation for medical students, but also in Continuing Professional Development groups for experienced doctors in practice.Patients with chronic pain are common in general practice [1]. In this paper chronic pain is defined as diffuse musculoskeletal pain associated with neither inflammatory diseases nor cancer. Chronic pain patients are considered a challenge by doctors [1-9]. Suspicion, failure and lack of power characterize doctors' relationships with these patients. Doctors feel suspicious when patients benefit from being ill and when biomedical explanations do not match patients' experience [2-4,6,7]. Doctors fear failure when neither cure, nor improvement nor consolat
Oxygenation effect of interventional lung assist in a lavage model of acute lung injury: a prospective experimental study
Günther Zick, Inéz Frerichs, Dirk Sch?dler, Gunnar Schmitz, Sven Pulletz, Erol Cavus, Felix Wachtler, Jens Scholz, Norbert Weiler
Critical Care , 2006, DOI: 10.1186/cc4889
Abstract: The study was designed as a prospective experimental study. The experiments were performed on seven pigs (48–60 kg body weight). The pigs were anesthetized and mechanically ventilated. Both femoral arteries and one femoral vein were cannulated and connected with ILA. Acute lung injury was induced by repeated bronchoalveolar lavage until the arterial partial pressure of O2 was lower than 100 Torr for at least 30 minutes during ventilation with 100% O2.ILA was applied with different blood flow rates through either one or both femoral arteries. Measurements were repeated at different degrees of pulmonary gas exchange impairment with the pulmonary venous admixture ranging from 35.0% to 70.6%. The mean (± standard deviation) blood flow through ILA was 15.5 (± 3.9)% and 21.7 (± 4.9)% of cardiac output with one and both arteries open, respectively. ILA significantly increased the arterial partial pressure of O2 from 64 (± 13) Torr to 71 (± 14) Torr and 74 (± 17) Torr with blood flow through one and both femoral arteries, respectively. O2 delivery through ILA increased with extracorporeal shunt flow (36 (± 14) ml O2/min versus 47 (± 17) ml O2/min) and reduced arterialization of the inlet blood. Pulmonary artery pressures were significantly reduced when ILA was in operation.Oxygenation is increased by ILA in severe lung injury. This effect is significant but small. The results indicate that the ILA use may not be justified if the improvement of oxygenation is the primary therapy goal.The mortality of patients with acute respiratory distress syndrome (ARDS) has remained high at about 30–50% despite all efforts in research and treatment [1]. Different strategies of mechanical ventilation focusing on the avoidance of ventilator-induced lung injury [2,3] and on the recruitment of diseased lung areas [4,5] are considered in the management of respiratory failure. Additional approaches applied are prone positioning [6], high-frequency oscillatory ventilation [7,8] and extracorporea
Page 1 /30964
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.