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Search Results: 1 - 10 of 5317 matches for " Albert Cardona "
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A high-level 3D visualization API for Java and ImageJ
Benjamin Schmid, Johannes Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-274
Abstract: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts.Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de webcite.Life sciences are experiencing an increasing demand for scientific image processing. Images are the primary data of developmental and cell biology. The number of images is exploding with the availability of high-throughput and high-resolution technologies. The acquisition of large three-dimensional (3D) data sets, often as time series (4D), has become the new standard.The first step in the analysis of biological image data is its visual inspection. In addition to the general requirement for visualization, the unique characteristics of each data set may demand specialized analysis. The development of novel analytical tools is greatly facilitated by the existence of well-documented software libraries. These libraries must provide (1) means to load and save any of the large diversity of image file formats; (2) implementations for computer vision algorithms; and (3) graphical user interfaces for data access by a human operator.We have identified a lack of accessible 3D/4D visua
A Tolerant Edit Distance for Evaluation and Training of Electron Microscopy Reconstruction Algorithms
Jan Funke,Jonas Klein,Albert Cardona,Matthew Cook
Computer Science , 2015,
Abstract: We present a measure to compare the labeling of automatic neuron reconstruction methods against ground truth. This measure, which we call tolerant edit distance (TED), is motivated by two observations: (1) Some errors, like small boundary shifts, are tolerable in practice. Which errors are tolerable is application dependent and should be a parameter of the measure. (2) Non-tolerable errors have to be corrected manually. The time needed to do so should be reflected by the error measure and minimized during training. The TED finds the minimal weighted sum of split and merge errors exceeding a given tolerance criterion, and thus provides a time-to-fix estimate. Our measure works on both isotropic and anisotropic EM datasets, the results are intuitive, and errors can be localized in the volume. We also present a structured learning framework for assignment models for anisotropic neuron reconstruction and show how this framework can be used to minimize the TED on annotated training samples. Evaluated on two publicly available EM-datasets, our method shows consistently higher reconstruction accuracy, even on pre-existing measures, than other current learning methods. Furthermore, we show how an appropriately defined tolerance criterion allows us to train on skeleton (i.e., non-volumetric) annotations, which are much faster to obtain in practice.
An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy
Albert Cardona,Stephan Saalfeld,Stephan Preibisch,Benjamin Schmid,Anchi Cheng,Jim Pulokas,Pavel Tomancak,Volker Hartenstein
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000502
Abstract: The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.
An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy
Albert Cardona,Stephan Saalfeld,Stephan Preibisch,Benjamin Schmid,Anchi Cheng,Jim Pulokas,Pavel Tomancak,Volker Hartenstein
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000502
Abstract: The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.
Multi-Hypothesis CRF-Segmentation of Neural Tissue in Anisotropic EM Volumes
Jan Funke,Bj?rn Andres,Fred Hamprecht,Albert Cardona,Matthew Cook
Computer Science , 2011,
Abstract: We present an approach for the joint segmentation and grouping of similar components in anisotropic 3D image data and use it to segment neural tissue in serial sections electron microscopy (EM) images. We first construct a nested set of neuron segmentation hypotheses for each slice. A conditional random field (CRF) then allows us to evaluate both the compatibility of a specific segmentation and a specific inter-slice assignment of neuron candidates with the underlying observations. The model is solved optimally for an entire image stack simultaneously using integer linear programming (ILP), which yields the maximum a posteriori solution in amortized linear time in the number of slices. We evaluate the performance of our approach on an annotated sample of the Drosophila larva neuropil and show that the consideration of different segmentation hypotheses in each slice leads to a significant improvement in the segmentation and assignment accuracy.
Inverse Problem on Heat Conduction in Heterogeneous Medium  [PDF]
Albert Schwab
American Journal of Computational Mathematics (AJCM) , 2014, DOI: 10.4236/ajcm.2014.41003
Abstract:

Under consideration is a nonclassical stationary problem on heat conduction in a body with the pre-set surface temperature and heat flow. The body contains inclusions at unknown locations and with unknown boundaries. The body and inclusions have different constant thermal conductivities. The author explores the possibility of locating inclusions. The article presents an integral criterion based on which a few statements on identification of inclusions in a body are proved.

Post Mid-Staffordshire Inquiries Reaction, in and about the National Health Service (NHS), England. The Missing Pieces: Organizational, Care and Virtue Ethics Perspectives  [PDF]
Albert Coleman
International Journal of Clinical Medicine (IJCM) , 2014, DOI: 10.4236/ijcm.2014.516131
Abstract:

The release of the Mid Staffordshire hospital report otherwise called the Francis report once again ignited the debate about the issue of abuse of especially vulnerable patients, while navigating the care pathway as inpatients in hospitals; within the National health service (NHS), England. Once more the official reaction from the NHS directorate is more “standards” to monitor failed standards in patient care. Of interest in the official responses so far, are the unheard voices addressing the issue of healthcare and organizational ethics concerns that need revisiting. This article seeks to revisit practice, systems and care issues leading to incidents of the type of the Staffordshire abuses, and the important but yet unheralded place of organizational and care ethics in helping to curb such abuses from re-occurring.

Road Traffic Accidents in Ghana: A Public Health Concern, and a Call for Action in Ghana, (and the Sub-Region)  [PDF]
Albert Coleman
Open Journal of Preventive Medicine (OJPM) , 2014, DOI: 10.4236/ojpm.2014.411092
Abstract: This paper highlights the increasing problem of road traffic accident (RTA) related morbidity and mortality in Ghana, and the public health measures needed to control the problem. Descriptive data in the public domain from statutory bodies and media houses reports on country RTA information, as well as academic papers on the problem, were used as source of information about the problem. The observed trend in Ghana indicates that RTA related fatalities and injuries continue to be increasing, as morbidity and mortality factors since the year 2000. Most of the remedial measures suggested in academic papers, and state agencies measures to curb the RTA trend in Ghana to date, have discussed the problem in terms of injury and safety issues/measures. This paper suggests that the increasing RTAs with associated morbidity and mortality in Ghana need to be looked at more as a public health problem and priority that requires prompt tackling using a public health problem orientated approach and measures, than just as a safety problem due to RTAs’, as is currently done.
New Wideband Notch Antennas for Communication Systems  [PDF]
Albert Sabban
Wireless Engineering and Technology (WET) , 2016, DOI: 10.4236/wet.2016.72008
Abstract: Wireless communication industry is in rapid growth in the last years. Due to the huge progress in development of communication systems in the last decade development of wideband communication systems is continuous growth. However, development of wideband efficient antennas is one of the major challenges in development of wideband wireless communication systems. Low cost compact antennas are crucial in the development of communication systems. Printed notch antennas and miniaturization techniques are employed to develop efficient compact notch antennas. Fractal technology is used to improve the electrical performance and efficiency of notch antennas. Design tradeoffs, computed and measured results of wideband notch antennas with high efficiency are presented in this paper. All antennas are analyzed by using 3D full-wave software. The paper presents new compact Ultra-Wideband notch antenna 1 GHz to 6 GHz, a wideband notch antenna 2.1 GHz to 7.8 GHz and a 5.8 GHz to 18 GHz fractal notch antenna.
Wearable Antenna Measurements in Vicinity of Human Body  [PDF]
Albert Sabban
Wireless Engineering and Technology (WET) , 2016, DOI: 10.4236/wet.2016.73010
Abstract: This paper presents measurements techniques of wearable antennas and RF medical systems in vicinity of human body. The antennas radiation characteristics on human body have been measured by using a phantom. The phantom electrical characteristics represent the human body electrical characteristics. The phantom has a cylindrical shape with a 40 cm diameter and a length of 1.5 m. The phantom electrical characteristics are similar to the human body electrical characteristics. The antenna under test was placed on the phantom during the measurements of the antennas radiation characteristics. The phantom was employed to compare the electrical performance of several new wearable antennas. The phantom was also employed to measure the electrical performance of several antenna belts in vicinity of human body. The results of antenna with thinner belt are better than the results of the same antenna array with thicker belt.
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