Accurate detection of dysmorphic nuclei using dynamic programming and supervised classification

A vast array of pathologies is typified by the presence of nuclei with an abnormal morphology. Dysmorphic nuclear phenotypes feature dramatic size changes or foldings, but also entail much subtler deviations such as nuclear protrusions called blebs. Due to their unpredictable size, shape and intensity, dysmorphic nuclei are often not accurately detected in standard image analysis routines. To enable accurate detection of dysmorphic nuclei in confocal and widefield fluorescence microscopy images, we have developed an automated segmentation algorithm, called Blebbed Nuclei Detector (BleND), which relies on two-pass thresholding for initial nuclear contour detection, and an optimal path finding algorithm, based on dynamic programming, for refining these contours. Using a robust error metric, we show that our method matches manual segmentation in terms of precision and outperforms state-of-the-art nuclear segmentation methods. Its high performance allowed for building and integrating a robust classifier that recognizes dysmorphic nuclei with an accuracy above 95%. The combined segmentation-classification routine is bound to facilitate nucleus-based diagnostics and enable real-time recognition of dysmorphic nuclei in intelligent microscopy workflows

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

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

Automatic recognition of fingerspelled words in British Sign Language

We investigate the problem of recognizing words from video, fingerspelled using the British Sign Language (BSL) fingerspelling alphabet. This is a challenging task since the BSL alphabet involves both hands occluding each other, and contains signs which are ambiguous from the observer’s viewpoint. The main contributions of our work include: (i) recognition based on hand shape alone, not requiring motion cues; (ii) robust visual features for hand shape recognition; (iii) scalability to large lexicon recognition with no re-training. We report results on a dataset of 1,000 low quality webcam videos of 100 words. The proposed method achieves a word recognition accuracy of 98.9%

Efficient Approach for OS-CFAR 2D Technique Using Distributive Histograms and Breakdown Point Optimal Concept applied to Acoustic Images

In this work, a new approach to improve the algorithmic efficiency of the Order Statistic-Constant False Alarm Rate (OS-CFAR) applied in two dimensions (2D) is presented. OS-CFAR is widely used in radar technology for detecting moving objects as well as in sonar technology for the relevant areas of segmentation and multi-target detection on the seafloor. OS-CFAR rank orders the samples obtained from a sliding window around a test cell to select a representative sample that is used to calculate an adaptive detection threshold maintaining a false alarm probability. Then, the test cell is evaluated to determine the presence or absence of a target based on the calculated threshold. The rank orders allows that OS-CFAR technique to be more robust in multi-target situations and less sensitive than other methods to the presence of the speckle noise, but requires higher computational effort. This is the bottleneck of the technique. Consequently, the contribution of this work is to improve the OS-CFAR 2D with the distributive histograms and the optimal breakdown point optimal concept, mainly from the standpoint of efficient computation. In this way, the OS-CFAR 2D on-line computation was improved, by means of speeding up the samples sorting problem through the improvement in the calculus of the statistics order. The theoretical algorithm analysis is presented to demonstrate the improvement of this approach. Also, this novel efficient OS-CFAR 2D was contrasted experimentally on acoustic images.Fil: Villar, Sebastian Aldo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Departamento de Electromecánica. Grupo INTELYMEC; ArgentinaFil: Menna, Bruno Victorio. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Departamento de Electromecánica. Grupo INTELYMEC; ArgentinaFil: Torcida, Sebastián. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Departamento de Matemática; ArgentinaFil: Acosta, Gerardo Gabriel. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Departamento de Electromecánica. Grupo INTELYMEC; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires; Argentin