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.esSupplementary information: Supplementary data are available at Bioinformatics online.

The analysis of digital video output enables the non-invasive screening of various active biological processes. For the monitoring and computing of the beating parameters of cardiomyocytes in vitro, CB Analyser (cardiomyocyte beating analyser) software was developed. This software is based on image analysis of the video recording of beating cardiomyocytes. CB Analyser was tested using cardiomyocytes derived from mouse embryonic stem cells at different stages of cardiomyogenesis. We observed that during differentiation (from day 18), the beat peak width decreased, which corresponded to the increased speed of an individual pulse. However, the beating frequency did not change. Further, the effects of epinephrine modulating mature cardiomyocyte functions were tested to validate the CB Analyser analysis. In conclusion, data show that CB Analyser is a useful tool for evaluating the functions of both developing and mature cardiomyocytes under various conditions in vitro.

No abstract

In this article, we propose a method for computing convolution of large 3D images. The convolution is performed in a frequency domain using a convolution theorem. The algorithm is accelerated on a graphic card by means of the CUDA parallel computing model. Convolution is decomposed in a frequency domain using the decimation in frequency algorithm. We pay attention to keeping our approach efficient in terms of both time and memory consumption and also in terms of memory transfers between CPU and GPU which have a significant inuence on overall computational time. We also study the implementation on multiple GPUs and compare the results between the multi-GPU and multi-CPU implementations.

Linear morphological openings and closings are important non-linear operators from mathematical morphology. In practical applications, many different orientations of digital line segments must typically be considered. In this paper, we (1) review efficient sequential as well as parallel algorithms for the computation of linear openings and closings, (2) compare the performance of CPU implementations of four state-of-the-art algorithms, (3) describe GPU implementations of two recent efficient algorithms allowing arbitrary orientation of the line segments, (4) propose, as the main contribution, an efficient and optimized GPU implementation of linear openings, and (5) compare the performance of all implementations on real images from various applications. From our experimental results, it turned out that the proposed GPU implementation is suitable for applications with large, industrial images, running under severe timing constraints.