1,328 research outputs found
DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images
Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License
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The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes
The signaling network of the unfolded protein response (UPR) adjusts the protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined the in-situ structure of IRE1α foci by cryogenic correlated light and electron microscopy (cryo-CLEM), combined with electron cryo-tomography (cryo-ET) and complementary immuno-electron microscopy. IRE1α oligomers localize to a network of narrow anastomosing ER tubes (diameter ~28 nm) with complex branching. The lumen of the tubes contains protein filaments, likely composed of linear arrays of IRE1α lumenal domain dimers, arranged in two intertwined, left-handed helices. Our findings define a previously unrecognized ER subdomain and suggest positive feedback in IRE1 signaling
Deciphering hierarchical organization of topologically associated domains through change-point testing.
BACKGROUND: The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them.
RESULTS: We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions.
CONCLUSIONS: HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions
Brain Tumor Segmentation with Deep Neural Networks
In this paper, we present a fully automatic brain tumor segmentation method
based on Deep Neural Networks (DNNs). The proposed networks are tailored to
glioblastomas (both low and high grade) pictured in MR images. By their very
nature, these tumors can appear anywhere in the brain and have almost any kind
of shape, size, and contrast. These reasons motivate our exploration of a
machine learning solution that exploits a flexible, high capacity DNN while
being extremely efficient. Here, we give a description of different model
choices that we've found to be necessary for obtaining competitive performance.
We explore in particular different architectures based on Convolutional Neural
Networks (CNN), i.e. DNNs specifically adapted to image data.
We present a novel CNN architecture which differs from those traditionally
used in computer vision. Our CNN exploits both local features as well as more
global contextual features simultaneously. Also, different from most
traditional uses of CNNs, our networks use a final layer that is a
convolutional implementation of a fully connected layer which allows a 40 fold
speed up. We also describe a 2-phase training procedure that allows us to
tackle difficulties related to the imbalance of tumor labels. Finally, we
explore a cascade architecture in which the output of a basic CNN is treated as
an additional source of information for a subsequent CNN. Results reported on
the 2013 BRATS test dataset reveal that our architecture improves over the
currently published state-of-the-art while being over 30 times faster
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Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin
A number of structural and functional subnuclear compartments have been described, including regions
exclusive of chromosomes previously hypothesized to form
a reactive nuclear space. We have now explored this
accessible nuclear space and interchromosomal
nucleoplasmic domains experimentally using Xenopus
vimentin engineered to contain a nuclear localization signal
(NLS-vimentin). In stably transfected human cells
incubated at 37°C, the NLS-vimentin formed a restricted
number of intranuclear speckles. At 28°C, the optimal
temperature for assembly of the amphibian protein, NLSvimentin
progressively extended with time out from the
speckles into strictly orientated intranuclear filamentous
arrays. This enabled us to observe the development of a
system of interconnecting channel-like areas. Quantitative
analysis based on 3-D imaging microscopy revealed that
these arrays were localized almost exclusively outside of
chromosome territories. During mitosis the filaments
disassembled and dispersed throughout the cytoplasm,
while in anaphase-telophase the vimentin was recruited
back into the nucleus and reassembled into filaments at the
chromosome surfaces, in distributions virtually identical to
those observed in the previous interphase. The filaments
also colocalized with specific nuclear RNAs, coiled bodies
and PML bodies, all situated outside of chromosome
territories, thereby interlinking these structures. This
strongly implies that these nuclear entities coexist in the
same interconnected nuclear compartment. The
assembling NLS-vimentin is restricted to and can be used
to delineate, at least in part, the formerly proposed
reticular interchromosomal domain compartment (ICD).
The properties of NLS-vimentin make it an excellent tool
for performing structural and functional studies on this
compartment
The Topology ToolKit
This system paper presents the Topology ToolKit (TTK), a software platform
designed for topological data analysis in scientific visualization. TTK
provides a unified, generic, efficient, and robust implementation of key
algorithms for the topological analysis of scalar data, including: critical
points, integral lines, persistence diagrams, persistence curves, merge trees,
contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots,
Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due
to a tight integration with ParaView. It is also easily accessible to
developers through a variety of bindings (Python, VTK/C++) for fast prototyping
or through direct, dependence-free, C++, to ease integration into pre-existing
complex systems. While developing TTK, we faced several algorithmic and
software engineering challenges, which we document in this paper. In
particular, we present an algorithm for the construction of a discrete gradient
that complies to the critical points extracted in the piecewise-linear setting.
This algorithm guarantees a combinatorial consistency across the topological
abstractions supported by TTK, and importantly, a unified implementation of
topological data simplification for multi-scale exploration and analysis. We
also present a cached triangulation data structure, that supports time
efficient and generic traversals, which self-adjusts its memory usage on demand
for input simplicial meshes and which implicitly emulates a triangulation for
regular grids with no memory overhead. Finally, we describe an original
software architecture, which guarantees memory efficient and direct accesses to
TTK features, while still allowing for researchers powerful and easy bindings
and extensions. TTK is open source (BSD license) and its code, online
documentation and video tutorials are available on TTK's website
Robust laparoscopic instruments tracking using colored strips
To assist surgeons in the acquisition of the required skills for the proper execution of the laparoscopic procedure, surgical simulators are used. During training with simulators it is useful to provide a surgical performance quantitative evaluation. Recent research works showed that such evaluation can be obtained by tracking the laparoscopic instruments, using only the images provided by the laparoscope and without hindering the surgical scene. In this work the state of the art method is improved so that a robust tracking can run even with the noisy background provided by realistic simulators. The method was validated by comparison with the tracking of a â\u80\u9cchess-boardâ\u80\u9d pattern and following tests were performed to check the robustness of the developed algorithm. Despite the noisy environment, the implemented method was found to be able to track the tip of the surgical instrument with a good accuracy compared to the other studies in the literature
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