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.

This analysis describes the results of three Cell Tracking Challenge editions for examining the performance of cell segmentation and tracking algorithms and provides practical feedback for users and developers. We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.

Motivation: Automatic tracking of cells in multidimensional time-lapse fluorescence microscopy is an important task in many biomedical applications. A novel framework for objective evaluation of cell tracking algorithms has been established under the auspices of the IEEE International Symposium on Biomedical Imaging 2013 Cell Tracking Challenge. In this article, we present the logistics, datasets, methods and results of the challenge and lay down the principles for future uses of this benchmark. Results: The main contributions of the challenge include the creation of a comprehensive video dataset repository and the definition of objective measures for comparison and ranking of the algorithms. With this benchmark, six algorithms covering a variety of segmentation and tracking paradigms have been compared and ranked based on their performance on both synthetic and real datasets. Given the diversity of the datasets, we do not declare a single winner of the challenge. Instead, we present and discuss the results for each individual dataset separately. Availability and implementation: The challenge Web site (http://www.codesolorzano.com/celltrackingchallenge) provides access to the training and competition datasets, along with the ground truth of the training videos. It also provides access to Windows and Linux executable files of the evaluation software and most of the algorithms that competed in the challenge. Contact:codesolorzano@unav.es Supplementary information: Supplementary data are available at Bioinformatics online.

It has been shown that employing multiple atlas images improves segmentation accuracy in atlas-based medical image segmentation. Each atlas image is registered to the target image independently and the calculated transformation is applied to the segmentation of the atlas image to obtain a segmented version of the target image. Several independent candidate segmentations result from the process, which must be somehow combined into a single final segmentation. Majority voting is the generally used rule to fuse the segmentations, but more sophisticated methods have also been proposed. In this paper, we show that the use of global weights to ponderate candidate segmentations has a major limitation. As a means to improve segmentation accuracy, we propose the generalized local weighting voting method. Namely, the fusion weights adapt voxel-by-voxel according to a local estimation of segmentation performance. Using digital phantoms and MR images of the human brain, we demonstrate that the performance of each combination technique depends on the gray level contrast characteristics of the segmented region, and that no fusion method yields better results than the others for all the regions. In particular, we show that local combination strategies outperform global methods in segmenting high-contrast structures, while global techniques are less sensitive to noise when contrast between neighboring structures is low. We conclude that, in order to achieve the highest overall segmentation accuracy, the best combination method for each particular structure must be selected.

Miguel Galarraga, Javier Campión, Arrate Muñoz-Barrutia, Noemí Boqué, Haritz Moreno, José Alfredo Martínez, Fermín Milagro, Carlos Ortiz-de-Solórzano