Extracting 3D parametric curves from 2D images of Helical objects

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively

Morphological operations in image processing and analysis

Morphological operations applied in image processing and analysis are becoming increasingly important in today\u27s technology. Morphological operations which are based on set theory, can extract object features by suitable shape (structuring elements). Morphological filters are combinations of morphological operations that transform an image into a quantitative description of its geometrical structure which based on structuring elements. Important applications of morphological operations are shape description, shape recognition, nonlinear filtering, industrial parts inspection, and medical image processing. In this dissertation, basic morphological operations are reviewed, algorithms and theorems are presented for solving problems in distance transformation, skeletonization, recognition, and nonlinear filtering. A skeletonization algorithm using the maxima-tracking method is introduced to generate a connected skeleton. A modified algorithm is proposed to eliminate non-significant short branches. The back propagation morphology is introduced to reach the roots of morphological filters in only two-scan. The definitions and properties of back propagation morphology are discussed. The two-scan distance transformation is proposed to illustrate the advantage of this new definition. G-spectrum (geometric spectrum) which based upon the cardinality of a set of non-overlapping segments in an image using morphological operations is presented to be a useful tool not only for shape description but also for shape recognition. The G-spectrum is proven to be translation-, rotation-, and scaling-invariant. The shape likeliness based on G-spectrum is defined as a measurement in shape recognition. Experimental results are also illustrated. Soft morphological operations which are found to be less sensitive to additive noise and to small variations are the combinations of order statistic and morphological operations. Soft morphological operations commute with thresholding and obey threshold superposition. This threshold decomposition property allows gray-scale signals to be decomposed into binary signals which can be processed by only logic gates in parallel and then binary results can be combined to produce the equivalent output. Thus the implementation and analysis of function-processing soft morphological operations can be done by focusing only on the case of sets which not only are much easier to deal with because their definitions involve only counting the points instead of sorting numbers, but also allow logic gates implementation and parallel pipelined architecture leading to real-time implementation. In general, soft opening and closing are not idempotent operations, but under some constraints the soft opening and closing can be idempotent and the proof is given. The idempotence property gives us the idea of how to choose the structuring element sets and the value of index such that the soft morphological filters will reach the root signals without iterations. Finally, summary and future research of this dissertation are provided

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

A novel shape descriptor based on empty morphological skeleton

Los Alamitos, US

Correcting curvature-density effects in the Hamilton-Jacobi skeleton

The Hainilton-Jacobi approach has proven to be a powerful and elegant method for extracting the skeleton of two-dimensional (2-D) shapes. The approach is based on the observation that the normalized flux associated with the inward evolution of the object boundary at nonskeletal points tends to zero as the size of the integration area tends to zero, while the flux is negative at the locations of skeletal points. Nonetheless, the error in calculating the flux on the image lattice is both limited by the pixel resolution and also proportional to the curvature of the boundary evolution front and, hence, unbounded near endpoints. This makes the exact location of endpoints difficult and renders the performance of the skeleton extraction algorithm dependent on a threshold parameter. This problem can be overcome by using interpolation techniques to calculate the flux with subpixel precision. However, here, we develop a method for 2-D skeleton extraction that circumvents the problem by eliminating the curvature contribution to the error. This is done by taking into account variations of density due to boundary curvature. This yields a skeletonization algorithm that gives both better localization and less susceptibility to boundary noise and parameter choice than the Hamilton-Jacobi method

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd

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