21 research outputs found
Spatiotemporal Identification of Cell Divisions Using Symmetry Properties in Time-Lapse Phase Contrast Microscopy
A variety of biological and pharmaceutical studies, such as for anti-cancer drugs, require the quantification of cell responses over long periods of time. This is performed with time-lapse video microscopy that gives a long sequence of frames. For this purpose, phase contrast imaging is commonly used since it is minimally invasive. The cell responses of interest in this study are the mitotic cell divisions. Their manual measurements are tedious, subjective, and restrictive. This study introduces an automated method for these measurements. The method starts with preprocessing for restoration and reconstruction of the phase contrast time-lapse sequences. The data are first restored from intensity non-uniformities. Subsequently, the circular symmetry of the contour of the mitotic cells in phase contrast images is used by applying a Circle Hough Transform (CHT) to reconstruct the entire cells. The CHT is also enhanced with the ability to “vote” exclusively towards the center of curvature. The CHT image sequence is then registered for misplacements between successive frames. The sequence is subsequently processed to detect cell centroids in individual frames and use them as starting points to form spatiotemporal trajectories of cells along the positive as well as along the negative time directions, that is, anti-causally. The connectivities of different trajectories enhanced by the symmetry of the trajectories of the daughter cells provide as topological by-products the events of cell divisions together with the corresponding entries into mitoses as well as exits from cytokineses. The experiments use several experimental video sequences from three different cell lines with many cells undergoing mitoses and divisions. The quantitative validations of the results of the processing demonstrate the high performance and efficiency of the method
A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction
Automatic cell segmentation and tracking enables to gain quantitative insights into the processes driving cell migration. To investigate new data with minimal manual effort, cell tracking algorithms should be easy to apply and reduce manual curation time by providing automatic correction of segmentation errors. Current cell tracking algorithms, however, are either easy to apply to new data sets but lack automatic segmentation error correction, or have a vast set of parameters that needs either manual tuning or annotated data for parameter tuning. In this work, we propose a tracking algorithm with only few manually tunable parameters and automatic segmentation error correction. Moreover, no training data is needed. We compare the performance of our approach to three well-performing tracking algorithms from the Cell Tracking Challenge on data sets with simulated, degraded segmentation—including false negatives, over- and under-segmentation errors. Our tracking algorithm can correct false negatives, over- and under-segmentation errors as well as a mixture of the aforementioned segmentation errors. On data sets with under-segmentation errors or a mixture of segmentation errors our approach performs best. Moreover, without requiring additional manual tuning, our approach ranks several times in the top 3 on the 6(th) edition of the Cell Tracking Challenge
Local cellular neighbourhood controls proliferation in cell competition
Cell competition is a quality control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterise interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep learning image analysis to decipher how single-cell behaviour determines tissue make-up during competition. Using our high-throughput analysis pipeline, we show that competitive interactions between MDCK wild-type cells and cells depleted of the polarity protein scribble are governed by differential sensitivity to local density and the cell-type of each cell's neighbours. We find that local density has a dramatic effect on the rate of division and apoptosis under competitive conditions. Strikingly, our analysis reveals that proliferation of the winner cells is upregulated in neighbourhoods mostly populated by loser cells. These data suggest that tissue-scale population shifts are strongly affected by cellular-scale tissue organisation. We present a quantitative mathematical model that demonstrates the effect of neighbour cell-type dependence of apoptosis and division in determining the fitness of competing cell lines
Conference of Advance Research and Innovation (ICARI-2014) 118 ICARI
Abstract With the advent of highly advanced optics and imaging system, currently biological research has reached a stage where scientists can study biological entities and processes at molecular and cellular-level in real time. However, a single experiment consists of hundreds and thousands of parameters to be recorded and a large population of microscopic objects to be tracked. Thus, making manual inspection of such events practically impossible. This calls for an approach to computer-vision based automated tracking and monitoring of cells in biological experiments. This technology promises to revolutionize the research in cellular biology and medical science which includes discovery of diseases by tracking the process in cells, development of therapy and drugs and the study of microscopic biological elements. This article surveys the recent literature in the area of computer vision based automated cell tracking. It discusses the latest trends and successes in the development and introduction of automated cell tracking techniques and systems
An objective comparison of cell-tracking algorithms
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
Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution
Live Cell Imaging and High Throughput Screening are rapidly evolving
techniques and have found many applications in recent years. Modern microscopy enables the visualisation of internal changes in the cell through the
use of
fluorescently tagged proteins which can be targeted to specific cellular
components.
A system is presented here which is designed to track cells at low temporal
resolution within large populations, and to extract
fluorescence data which
allows relative expression rates of tagged proteins to be monitored.
Cell detection and tracking are performed as separate steps, and several
methods are evaluated for suitability using timeseries images of Hoechst-stained
C2C12 mouse mesenchymal stem cells. The use of Hoechst staining ensures
cell nuclei are visible throughout a time-series. Dynamic features, including
a characteristic change in Hoechst
fluorescence intensity during chromosome
condensation, are used to identify cell divisions and resulting daughter cells.
The ability to detect cell division is integrated into the tracking, aiding
lineage construction. To establish the efficiency of the method, synthetic cell
images have been produced and used to evaluate cell detection accuracy. A
validation framework is created which allows the accuracy of the automatic
segmentation and tracking systems to be measured and compared against
existing state of the art software, such as CellProfiler. Basic tracking methods,
including nearest-neighbour and cell-overlap, are provided as a baseline to
evaluate the performance of more sophisticated methods.
The software is demonstrated on a number of biological systems, starting
with a study of different control elements of the Msx1 gene, which regulates
differentiation of mesenchymal stem cells. Expression is followed through
multiple lineages to identify asymmetric divisions which may be due to cell
differentiation.
The lineage construction methods are applied to Schizosaccharomyces pombe
time-series image data, allowing the extraction of generation lengths for individual cells. Finally a study is presented which examines correlations between
the circadian and cell cycles. This makes use of the recently developed FUCCI
cell cycle markers which, when used in conjunction with a circadian indicator
such as Rev-erbα-Venus, allow simultaneous measurements of both cycles