1,167 research outputs found
Active skeleton for bacteria modeling
The investigation of spatio-temporal dynamics of bacterial cells and their
molecular components requires automated image analysis tools to track cell
shape properties and molecular component locations inside the cells. In the
study of bacteria aging, the molecular components of interest are protein
aggregates accumulated near bacteria boundaries. This particular location makes
very ambiguous the correspondence between aggregates and cells, since computing
accurately bacteria boundaries in phase-contrast time-lapse imaging is a
challenging task. This paper proposes an active skeleton formulation for
bacteria modeling which provides several advantages: an easy computation of
shape properties (perimeter, length, thickness, orientation), an improved
boundary accuracy in noisy images, and a natural bacteria-centered coordinate
system that permits the intrinsic location of molecular components inside the
cell. Starting from an initial skeleton estimate, the medial axis of the
bacterium is obtained by minimizing an energy function which incorporates
bacteria shape constraints. Experimental results on biological images and
comparative evaluation of the performances validate the proposed approach for
modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the
proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical
Engineering: Imaging and Visualizationto appear i
Subset Warping: Rubber Sheeting with Cuts
Image warping, often referred to as "rubber sheeting" represents the deformation of a domain image space into a range image space. In this paper, a technique is described which extends the definition of a rubber-sheet transformation to allow a polygonal region to be warped into one or more subsets of itself, where the subsets may be multiply connected. To do this, it constructs a set of "slits" in the domain image, which correspond to discontinuities in the range image, using a technique based on generalized Voronoi diagrams. The concept of medial axis is extended to describe inner and outer medial contours of a polygon. Polygonal regions are decomposed into annular subregions, and path homotopies are introduced to describe the annular subregions. These constructions motivate the definition of a ladder, which guides the construction of grid point pairs necessary to effect the warp itself
Unwind: Interactive Fish Straightening
The ScanAllFish project is a large-scale effort to scan all the world's
33,100 known species of fishes. It has already generated thousands of
volumetric CT scans of fish species which are available on open access
platforms such as the Open Science Framework. To achieve a scanning rate
required for a project of this magnitude, many specimens are grouped together
into a single tube and scanned all at once. The resulting data contain many
fish which are often bent and twisted to fit into the scanner. Our system,
Unwind, is a novel interactive visualization and processing tool which
extracts, unbends, and untwists volumetric images of fish with minimal user
interaction. Our approach enables scientists to interactively unwarp these
volumes to remove the undesired torque and bending using a piecewise-linear
skeleton extracted by averaging isosurfaces of a harmonic function connecting
the head and tail of each fish. The result is a volumetric dataset of a
individual, straight fish in a canonical pose defined by the marine biologist
expert user. We have developed Unwind in collaboration with a team of marine
biologists: Our system has been deployed in their labs, and is presently being
used for dataset construction, biomechanical analysis, and the generation of
figures for scientific publication
Skeleton as a probe of the cosmic web: the 2D case
We discuss the skeleton as a probe of the filamentary structures of a 2D
random field. It can be defined for a smooth field as the ensemble of pairs of
field lines departing from saddle points, initially aligned with the major axis
of local curvature and connecting them to local maxima. This definition is thus
non local and makes analytical predictions difficult, so we propose a local
approximation: the local skeleton is given by the set of points where the
gradient is aligned with the local curvature major axis and where the second
component of the local curvature is negative.
We perform a statistical analysis of the length of the total local skeleton,
chosen for simplicity as the set of all points of space where the gradient is
either parallel or orthogonal to the main curvature axis. In all our numerical
experiments, which include Gaussian and various non Gaussian realizations such
as \chi^2 fields and Zel'dovich maps, the differential length is found within a
normalization factor to be very close to the probability distribution function
of the smoothed field. This is in fact explicitly demonstrated in the Gaussian
case.
This result might be discouraging for using the skeleton as a probe of non
Gausiannity, but our analyses assume that the total length of the skeleton is a
free, adjustable parameter. This total length could in fact be used to
constrain cosmological models, in CMB maps but also in 3D galaxy catalogs,
where it estimates the total length of filaments in the Universe. Making the
link with other works, we also show how the skeleton can be used to study the
dynamics of large scale structure.Comment: 15 pages, 11 figures, submitted to MNRA
Reconstruction of Three-Dimensional Blood Vessel Model Using Fractal Interpolation
Fractal method is used in the image processing and studying the irregular and the complex shapes in the image. It is also used in the reconstruction and smoothing of one-, two-, and three-dimensional data. In this chapter, we present an interpolating fractal algorithm to reconstruct 3D blood vessels. Firstly, the proposed method determines the blood vessel centerline from the 2D retina image, and then it uses the Douglas-Peucker algorithm to detect the control points. Secondly, we use the 3D fractal interpolation and iterated function systems for the visualization and reconstruction of these blood vessels. The results showed that the obtained reduction rate is between 71 and 94% depending on the tolerance value. The 3D blood vessels model can be reconstructed efficiently by using the 3D fractal interpolation method
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