The first community competition designed to objectively compare the performance of particle tracking algorithms provides valuable practical information for both users and developers. Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.

In image processing, the rapid approximate solution of variational problems involving generic data-fitting terms is often of practical relevance, for example in real-time applications. Variational solvers based on diffusion schemes or the Euler-Lagrange equations are too slow and restricted in the types of data-fitting terms. Here, we present a filter-based approach to reduce variational energies that contain generic data-fitting terms, but are restricted to specific regularizations. Our approach is based on reducing the regularization part of the variational energy, while guaranteeing non-increasing total energy. This is applicable to regularization-dominated models, where the data-fitting energy initially increases, while the regularization energy initially decreases. We present fast discrete filters for regularizers based on Gaussian curvature, mean curvature, and total variation. These pixel-local filters can be used to rapidly reduce the energy of the full model. We prove the convergence of the resulting iterative scheme in a greedy sense, and we show several experiments to demonstrate applications in image-processing problems involving regularization-dominated variational models.

Local windows are routinely used in computer vision and almost without exception the center of the window is aligned with the pixels being processed. We show that this conventional wisdom is not universally applicable. When a pixel is on an edge, placing the center of the window on the pixel is one of the fundamental reasons that cause many filtering algorithms to blur the edges. Based on this insight, we propose a new Side Window Filtering (SWF) technique which aligns the window's side or corner with the pixel being processed. The SWF technique is surprisingly simple yet theoretically rooted and very effective in practice. We show that many traditional linear and nonlinear filters can be easily implemented under the SWF framework. Extensive analysis and experiments show that implementing the SWF principle can significantly improve their edge preserving capabilities and achieve state of the art performances in applications such as image smoothing, denoising, enhancement, structure-preserving texture-removing, mutual-structure extraction, and HDR tone mapping. In addition to image filtering, we further show that the SWF principle can be extended to other applications involving the use of a local window. Using colorization by optimization as an example, we demonstrate that implementing the SWF principle can effectively prevent artifacts such as color leakage associated with the conventional implementation. Given the ubiquity of window based operations in computer vision, the new SWF technique is likely to benefit many more applications.

One of the methods for stratifying different molecular classes of breast cancer is the Nottingham Prognostic Index Plus (NPI+) which uses breast cancer relevant biomarkers to stain tumour tissues prepared on tissue microarray (TMA). To determine the molecular class of the tumour, pathologists will have to manually mark the nuclei activity biomarkers through a microscope and use a semi-quantitative assessment method to assign a histochemical score (H-Score) to each TMA core. Manually marking positively stained nuclei is a time consuming, imprecise and subjective process which will lead to inter-observer and intra-observer discrepancies. In this paper, we present an end-to-end deep learning system which directly predicts the H-Score automatically. Our system imitates the pathologists’ decision process and uses one fully convolutional network (FCN) to extract all nuclei region (tumour and non-tumour), a second FCN to extract tumour nuclei region, and a multi-column convolutional neural network which takes the outputs of the first two FCNs and the stain intensity description image as input and acts as the high-level decision making mechanism to directly output the H-Score of the input TMA image. To the best of our knowledge, this is the first end-to-end system that takes a TMA image as input and directly outputs a clinical score. We will present experimental results which demonstrate that the H-Scores predicted by our model have very high and statistically significant correlation with experienced pathologists’ scores and that the H-Score discrepancy between our algorithm and the pathologists is on par with the inter-subject discrepancy between the pathologists.