A computational efficient external energy for active contour segmentation using edge propagation

Active contours or snakes are widely used for segmentation and tracking. We propose a new active contour model, which converges reliably even when the initialization is far from the object of interest. The proposed segmentation technique uses an external energy function where the energy slowly decreases in the vicinity of an edge. This new energy function is calculated using an efficient dual scan line algorithm. The proposed energy function is tested on computational speed, its effect on the convergence speed of the active contour and the segmentation result. The proposed method gets similar segmentation results as the gradient vector flow active contours, but the energy function needs much less time to calculate

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

Achieving the Way for Automated Segmentation of Nuclei in Cancer Tissue Images through Morphology-Based Approach: a Quantitative Evaluation

In this paper we address the problem of nuclear segmentation in cancer tissue images, that is critical for specific protein activity quantification and for cancer diagnosis and therapy. We present a fully automated morphology-based technique able to perform accurate nuclear segmentations in images with heterogeneous staining and multiple tissue layers and we compare it with an alternate semi-automated method based on a well established segmentation approach, namely active contours. We discuss active contours’ limitations in the segmentation of immunohistochemical images and we demonstrate and motivate through extensive experiments the better accuracy of our fully automated approach compared to various active contours implementations

Cell nuclei detection using globally optimal active contours with shape prior

Cell nuclei detection in fluorescent microscopic images is an important and time consuming task for a wide range of biological applications. Blur, clutter, bleed through and partial occlusion of nuclei make this a challenging task for automated detection of individual nuclei using image analysis. This paper proposes a novel and robust detection method based on the active contour framework. The method exploits prior knowledge of the nucleus shape in order to better detect individual nuclei. The method is formulated as the optimization of a convex energy function. The proposed method shows accurate detection results even for clusters of nuclei where state of the art methods fail

A fast external force field for parametric active contour segmentation

Active contours or snakes are widely used for segmentation and tracking. We propose a new active contour model, which converges reliably even when the initialization is far from the object of interest. The proposed segmentation technique uses an external energy function where the energy slowly decreases in the vicinity of an edge. Based on this energy a new external force field is defined. Both energy function and force field are calculated using an efficient dual scan line algorithm. The proposed force field is tested on computational speed, its effect on the convergence speed of the active contour and the segmentation result. The proposed method gets similar segmentation results as the gradient vector flow and vector field convolution active contours, but the force field needs significantly less time to calculate

Nowcasting Thunderstorms for Munich Airport

The successful demonstration and assessment of the DLR thunderstorm nowcasting algorithms at Munich Airport during two campaigns in the summers of 2010 and 2011 are described. The algorithms Cb-TRAM and Rad-TRAM, that detect, monitor, and forecast up to one hour (nowcast) thunderstorm cells from satellite and radar data, run in real time and provided new thunderstorm products for users at the airport. The products were presented on displays the users were already familiar with as well as on webpages designed by DLR. On the webpages, also additional information like measurements with DLR’s polarimetric radar and model forecasts was shown. Moreover, thunderstorm warnings were is-sued and sent via email to the users whenever a thunderstorm was detected in the terminal manoeu-vring area of the airport of Munich. The nowcasting skills of Rad-TRAM and Cb-TRAM are encouraging, especially for lead times up to 30 minutes, and the user feedback on the DLR thunderstorm products was very positive. The Rad-TRAM and Cb-TRAM products provide a good overview on the situation and its future development, and the thunderstorm warnings were very helpful for the collaborative decision making at the airport. However, some suggestions for improvements were made like the demand for nowcasts beyond one hour. This will be considered within the integrated weather forecast system, WxFUSION, which has been further developed during the campaigns

Towards a Unified Theory of Neocortex: Laminar Cortical Circuits for Vision and Cognition

A key goal of computational neuroscience is to link brain mechanisms to behavioral functions. The present article describes recent progress towards explaining how laminar neocortical circuits give rise to biological intelligence. These circuits embody two new and revolutionary computational paradigms: Complementary Computing and Laminar Computing. Circuit properties include a novel synthesis of feedforward and feedback processing, of digital and analog processing, and of pre-attentive and attentive processing. This synthesis clarifies the appeal of Bayesian approaches but has a far greater predictive range that naturally extends to self-organizing processes. Examples from vision and cognition are summarized. A LAMINART architecture unifies properties of visual development, learning, perceptual grouping, attention, and 3D vision. A key modeling theme is that the mechanisms which enable development and learning to occur in a stable way imply properties of adult behavior. It is noted how higher-order attentional constraints can influence multiple cortical regions, and how spatial and object attention work together to learn view-invariant object categories. In particular, a form-fitting spatial attentional shroud can allow an emerging view-invariant object category to remain active while multiple view categories are associated with it during sequences of saccadic eye movements. Finally, the chapter summarizes recent work on the LIST PARSE model of cognitive information processing by the laminar circuits of prefrontal cortex. LIST PARSE models the short-term storage of event sequences in working memory, their unitization through learning into sequence, or list, chunks, and their read-out in planned sequential performance that is under volitional control. LIST PARSE provides a laminar embodiment of Item and Order working memories, also called Competitive Queuing models, that have been supported by both psychophysical and neurobiological data. These examples show how variations of a common laminar cortical design can embody properties of visual and cognitive intelligence that seem, at least on the surface, to be mechanistically unrelated.National Science Foundation (SBE-0354378); Office of Naval Research (N00014-01-1-0624