5,104 research outputs found
Fast and robust curve skeletonization for real-world elongated objects
We consider the problem of extracting curve skeletons of three-dimensional,
elongated objects given a noisy surface, which has applications in agricultural
contexts such as extracting the branching structure of plants. We describe an
efficient and robust method based on breadth-first search that can determine
curve skeletons in these contexts. Our approach is capable of automatically
detecting junction points as well as spurious segments and loops. All of that
is accomplished with only one user-adjustable parameter. The run time of our
method ranges from hundreds of milliseconds to less than four seconds on large,
challenging datasets, which makes it appropriate for situations where real-time
decision making is needed. Experiments on synthetic models as well as on data
from real world objects, some of which were collected in challenging field
conditions, show that our approach compares favorably to classical thinning
algorithms as well as to recent contributions to the field.Comment: 47 pages; IEEE WACV 2018, main paper and supplementary materia
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
Disconnected Skeleton: Shape at its Absolute Scale
We present a new skeletal representation along with a matching framework to
address the deformable shape recognition problem. The disconnectedness arises
as a result of excessive regularization that we use to describe a shape at an
attainably coarse scale. Our motivation is to rely on the stable properties of
the shape instead of inaccurately measured secondary details. The new
representation does not suffer from the common instability problems of
traditional connected skeletons, and the matching process gives quite
successful results on a diverse database of 2D shapes. An important difference
of our approach from the conventional use of the skeleton is that we replace
the local coordinate frame with a global Euclidean frame supported by
additional mechanisms to handle articulations and local boundary deformations.
As a result, we can produce descriptions that are sensitive to any combination
of changes in scale, position, orientation and articulation, as well as
invariant ones.Comment: The work excluding {\S}V and {\S}VI has first appeared in 2005 ICCV:
Aslan, C., Tari, S.: An Axis-Based Representation for Recognition. In
ICCV(2005) 1339- 1346.; Aslan, C., : Disconnected Skeletons for Shape
Recognition. Masters thesis, Department of Computer Engineering, Middle East
Technical University, May 200
Using eSkel to Implement the Multiple Baseline Stereo Application
We give an overview of the Edinburgh Skeleton Library eSkel, a structured parallel programming library which offers a range of skeletal parallel programming constructs to the C/MPI programmer. Then we illustrate the efficacy of such a high level approach through an application of multiple baseline stereo. We describe the application and show different ways to introduce parallelism using algorithmic skeletons. Some performance results will be reported
Automated tracing of myelinated axons and detection of the nodes of Ranvier in serial images of peripheral nerves
The development of realistic neuroanatomical models of peripheral nerves for simulation purposes requires the reconstruction of the morphology of the myelinated fibres in the nerve, including their nodes of Ranvier. Currently, this information has to be extracted by semimanual procedures, which severely limit the scalability of the experiments. In this contribution, we propose a supervised machine learning approach for the detailed reconstruction of the geometry of fibres inside a peripheral nerve based on its high-resolution serial section images. Learning from sparse expert annotations, the algorithm traces myelinated axons, even across the nodes of Ranvier. The latter are detected automatically. The approach is based on classifying the myelinated membranes in a supervised fashion, closing the membrane gaps by solving an assignment problem, and classifying the closed gaps for the nodes of Ranvier detection. The algorithm has been validated on two very different datasets: (i) rat vagus nerve subvolume, SBFSEM microscope, 200 × 200 × 200 nm resolution, (ii) rat sensory branch subvolume, confocal microscope, 384 × 384 × 800 nm resolution. For the first dataset, the algorithm correctly reconstructed 88% of the axons (241 out of 273) and achieved 92% accuracy on the task of Ranvier node detection. For the second dataset, the gap closing algorithm correctly closed 96.2% of the gaps, and 55% of axons were reconstructed correctly through the whole volume. On both datasets, training the algorithm on a small data subset and applying it to the full dataset takes a fraction of the time required by the currently used semiautomated protocols. Our software, raw data and ground truth annotations are available at http://hci.iwr.uni-heidelberg.de/Benchmarks/. The development version of the code can be found at https://github.com/RWalecki/ATMA
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