Cell tracking
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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.
The Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present a significant number of improvements introduced in the challenge since our 2017 report. These include the creation of a new segmentation-only benchmark, the enrichment of the dataset repository with new datasets that increase its diversity and complexity, and the creation of a silver standard reference corpus based on the most competitive results, which will be of particular interest for data-hungry deep learning-based strategies. Furthermore, we present the up-to-date cell segmentation and tracking leaderboards, an in-depth analysis of the relationship between the performance of the state-of-the-art methods and the properties of the datasets and annotations, and two novel, insightful studies about the generalizability and the reusability of top-performing methods. These studies provide critical practical conclusions for both developers and users of traditional and machine learning-based cell segmentation and tracking algorithms.
Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs.
We present a fast and robust approach to tracking the evolving shape of whole fluorescent cells in time-lapse series. The proposed tracking scheme involves two steps. First, coherence-enhancing diffusion filtering is applied on each frame to reduce the amount of noise and enhance flow-like structures. Second, the cell boundaries are detected by minimizing the Chan-Vese model in the fast level set-like and graph cut frameworks. To allow simultaneous tracking of multiple cells over time, both frameworks have been integrated with a topological prior exploiting the object indication function. The potential of the proposed tracking scheme and the advantages and disadvantages of both frameworks are demonstrated on 2-D and 3-D time-lapse series of rat adipose-derived mesenchymal stem cells and human lung squamous cell carcinoma cells, respectively.
- MeSH
- buněčné jádro chemie MeSH
- buněčný tracking metody MeSH
- fluorescenční mikroskopie metody MeSH
- krysa rodu rattus MeSH
- lidé MeSH
- mezenchymální kmenové buňky cytologie MeSH
- nádorové buněčné linie MeSH
- počítačové zpracování obrazu metody MeSH
- tvar buňky fyziologie MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Noninvasive cellular imaging allows the real-time tracking of grafted cells as well as the monitoring of their migration. Several techniques for in vivo cellular imaging are available that permit the characterization of transplanted cells in a living organism, including magnetic resonance imaging (MRI), bioluminescence, positron emission tomography, and multiple photon microscopy. All of these methods, based on different principles, provide distinctive, usually complementary information. In this review, we will focus on cell tracking using MRI, since MRI is noninvasive, clinically transferable, and displays good resolution, ranging from 50microm in animal experiments up to 300microm using whole body clinical scanners. In addition to information about grafted cells, MRI provides information about the surrounding tissue (i.e., lesion size, edema, inflammation), which may negatively affect graft survival or the functional recovery of the tissue. Transplanted cells are labeled with MR contrast agents in vitro prior to transplantation in order to visualize them in the host tissue. The chapter will focus on the use of superparamagnetic iron oxide nanoparticles (SPIO), because they have strong effects on T2 relaxation yet do not affect cell viability, and will provide an overview of different modifications of SPIO and their use in MR tracking in living organisms.
- MeSH
- buněčné kultury MeSH
- financování organizované MeSH
- kontrastní látky chemie metabolismus MeSH
- kovové nanočástice chemie MeSH
- krysa rodu rattus MeSH
- kultivované buňky MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody přístrojové vybavení MeSH
- mezenchymální kmenové buňky cytologie fyziologie MeSH
- mícha anatomie a histologie metabolismus patologie MeSH
- mozek anatomie a histologie metabolismus patologie MeSH
- neurodegenerativní nemoci metabolismus patologie MeSH
- transplantace mezenchymálních kmenových buněk MeSH
- železité sloučeniny chemie MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- lidé MeSH
- zvířata MeSH
A better understanding of the molecular mechanisms leading to mast cell migration and chemotaxis is the long-term goal in mast cell research and is essential for comprehension of mast cell function in health and disease. Various techniques have been developed in recent decades for in vitro and in vivo assessment of mast cell motility and chemotaxis. In this chapter, three microscopy assays facilitating real-time quantification of mast cell chemotaxis and migration are described, focusing on individual cell tracking and data analysis.
- MeSH
- analýza buněčné migrace metody MeSH
- biotest metody MeSH
- buněčný tracking metody MeSH
- chemotaxe fyziologie MeSH
- fibronektiny metabolismus MeSH
- lidé MeSH
- mastocyty cytologie fyziologie MeSH
- mikroskopie metody MeSH
- myši MeSH
- počítačové systémy MeSH
- pohyb buněk fyziologie MeSH
- prostředí kontrolované MeSH
- sefarosa MeSH
- software MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A better understanding of the molecular mechanisms leading to mast cell migration and chemotaxis is the long-term goal in mast cell research and is essential for comprehension of mast cell function in health and disease. Various techniques have been developed in recent decades for in vitro and in vivo assessment of mast cell motility and chemotaxis. In this chapter three microscopy assays facilitating real-time quantification of mast cell chemotaxis and migration are described, focusing on individual cell tracking and data analysis.
- MeSH
- analýza buněčné migrace metody MeSH
- buněčné kultury přístrojové vybavení metody MeSH
- buněčný tracking metody MeSH
- chemotaktické faktory farmakologie MeSH
- chemotaxe MeSH
- kultivované buňky MeSH
- lidé MeSH
- mastocyty cytologie účinky léků fyziologie MeSH
- mikroskopie metody MeSH
- pohyb buněk * účinky léků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.
- MeSH
- antigeny virové imunologie MeSH
- dárci tkání MeSH
- dvojčata monozygotní MeSH
- imunizace metody MeSH
- lidé MeSH
- receptory antigenů T-buněk imunologie MeSH
- T-lymfocyty imunologie MeSH
- vakcína proti žluté zimnici imunologie MeSH
- vakcinace metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Chromosome architecture needs to be investigated in relation with the chemical function of DNA. The kinetics of gene expression, DNA replication, and repair are driven by the mechanisms by which a functional nuclear protein finds its substrate in the nucleus. Single-particle tracking (SPT) is a method to quantify fluorescent molecules dynamics from the tracks of the single molecules recorded by high-resolution microscopes. SPT offers direct observation of the movement and single-molecule resolution. Usually SPT is performed on membranes because of higher contrast. Here, we introduce a novel method to record the trajectories of weakly fluorescent molecules in the nucleus of living cells. I-SPT uses some specific detection and analysis tools to enable the computation of reliable statistics on nuclear particle movement.
Remarkable progress in various techniques of in vivo fluorescence microscopy has brought an urgent need for reliable markers for tracking cellular structures and processes. The goal of this manuscript is to describe unexplored effects of the FM (Fei Mao) styryl dyes, which are widely used probes that label processes of endocytosis and vesicle trafficking in eukaryotic cells. Although there are few reports on the effect of styryl dyes on membrane fluidity and the activity of mammalian receptors, FM dyes have been considered as reliable tools for tracking of plant endocytosis. Using plasma membrane-localized transporters for the plant hormone auxin in tobacco BY-2 and Arabidopsis thaliana cell suspensions, we show that routinely used concentrations of FM 4-64 and FM 5-95 trigger transient re-localization of these proteins, and FM 1-43 affects their activity. The active process of re-localization is blocked neither by inhibitors of endocytosis nor by cytoskeletal drugs. It does not occur in A. thaliana roots and depends on the degree of hydrophobicity (lipophilicity) of a particular FM dye. Our results emphasize the need for circumspection during in vivo studies of membrane proteins performed using simultaneous labelling with FM dyes.
- MeSH
- Arabidopsis cytologie MeSH
- buněčná membrána chemie MeSH
- buněčné linie MeSH
- endocytóza MeSH
- fluorescenční barviva farmakologie MeSH
- kvartérní amoniové sloučeniny farmakologie MeSH
- kyseliny indoloctové metabolismus MeSH
- pyridinové sloučeniny farmakologie MeSH
- rostlinné proteiny účinky léků MeSH
- transport proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
