30,183 research outputs found
J-PET Framework: Software platform for PET tomography data reconstruction and analysis
J-PET Framework is an open-source software platform for data analysis,
written in C++ and based on the ROOT package. It provides a common environment
for implementation of reconstruction, calibration and filtering procedures, as
well as for user-level analyses of Positron Emission Tomography data. The
library contains a set of building blocks that can be combined by users with
even little programming experience, into chains of processing tasks through a
convenient, simple and well-documented API. The generic input-output interface
allows processing the data from various sources: low-level data from the
tomography acquisition system or from diagnostic setups such as digital
oscilloscopes, as well as high-level tomography structures e.g. sinograms or a
list of lines-of-response. Moreover, the environment can be interfaced with
Monte Carlo simulation packages such as GEANT and GATE, which are commonly used
in the medical scientific community.Comment: 14 pages, 5 figure
Interactive visualisation and exploration of biological data
International audienceno abstrac
Streaming visualisation of quantitative mass spectrometry data based on a novel raw signal decomposition method
As data rates rise, there is a danger that informatics for high-throughput LC-MS becomes more opaque and inaccessible to practitioners. It is therefore critical that efficient visualisation tools are available to facilitate quality control, verification, validation, interpretation, and sharing of raw MS data and the results of MS analyses. Currently, MS data is stored as contiguous spectra. Recall of individual spectra is quick but panoramas, zooming and panning across whole datasets necessitates processing/memory overheads impractical for interactive use. Moreover, visualisation is challenging if significant quantification data is missing due to data-dependent acquisition of MS/MS spectra. In order to tackle these issues, we leverage our seaMass technique for novel signal decomposition. LC-MS data is modelled as a 2D surface through selection of a sparse set of weighted B-spline basis functions from an over-complete dictionary. By ordering and spatially partitioning the weights with an R-tree data model, efficient streaming visualisations are achieved. In this paper, we describe the core MS1 visualisation engine and overlay of MS/MS annotations. This enables the mass spectrometrist to quickly inspect whole runs for ionisation/chromatographic issues, MS/MS precursors for coverage problems, or putative biomarkers for interferences, for example. The open-source software is available from http://seamass.net/viz/
Continuous Multiclass Labeling Approaches and Algorithms
We study convex relaxations of the image labeling problem on a continuous
domain with regularizers based on metric interaction potentials. The generic
framework ensures existence of minimizers and covers a wide range of
relaxations of the originally combinatorial problem. We focus on two specific
relaxations that differ in flexibility and simplicity -- one can be used to
tightly relax any metric interaction potential, while the other one only covers
Euclidean metrics but requires less computational effort. For solving the
nonsmooth discretized problem, we propose a globally convergent
Douglas-Rachford scheme, and show that a sequence of dual iterates can be
recovered in order to provide a posteriori optimality bounds. In a quantitative
comparison to two other first-order methods, the approach shows competitive
performance on synthetical and real-world images. By combining the method with
an improved binarization technique for nonstandard potentials, we were able to
routinely recover discrete solutions within 1%--5% of the global optimum for
the combinatorial image labeling problem
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