Methods for Cell and Particle Tracking

Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.
Methods in enzymology (Impact Factor: 2.09). 12/2012; 504:183-200. DOI: 10.1016/B978-0-12-391857-4.00009-4
Source: PubMed


Achieving complete understanding of any living thing inevitably requires thorough analysis of both its anatomic and dynamic properties. Live-cell imaging experiments carried out to this end often produce massive amounts of time-lapse image data containing far more information than can be digested by a human observer. Computerized image analysis offers the potential to take full advantage of available data in an efficient and reproducible manner. A recurring task in many experiments is the tracking of large numbers of cells or particles and the analysis of their (morpho)dynamic behavior. In the past decade, many methods have been developed for this purpose, and software tools based on these are increasingly becoming available. Here, we survey the latest developments in this area and discuss the various computational approaches, software tools, and quantitative measures for tracking and motion analysis of cells and particles in time-lapse microscopy images.

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    • "Left epifluorescence picture; right total internal reflection fluorescence (TIRF) micrograph of the basal cell area (Color figure online) E. Merklinger et al.: No Evidence for Spontaneous Lipid Transfer… occurred. The movement of spots was manually tracked using the MTrackJ plugin (Meijering et al. 2012) for ImageJ applying centroid positioning within ROIs of 7 or 9 pixel diameter. Mean-square displacement (MSD) was calculated as described previously (Qian et al. 1991; Kusumi et al. 1993) for all spots within a 50 9 50 pixel ROI which were traceable for C20 frames before and after treatment. "
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    ABSTRACT: Non-vesicular lipid transport steps play a crucial role in lipid trafficking and potentially include spontaneous exchange. Since membrane contact facilitates this lipid transfer, it is most likely to occur at membrane contact sites (MCS). However, to date it is unknown whether closely attached biological membranes exchange lipids spontaneously. We have set up a system for studying the exchange of lipids at MCS formed between the endoplasmic reticulum (ER) and the plasma membrane. Contact sites were stably anchored and the lipids cholesterol and phosphatidylcholine (PC) were not capable of transferring spontaneously into the opposed bilayer. We conclude that physical contact between two associated biological membranes is not sufficient for transfer of the lipids PC and cholesterol.
    Journal of Membrane Biology 10/2015; DOI:10.1007/s00232-015-9845-2 · 2.46 Impact Factor
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    • "The last time point of the track is labeled with the particle number. The tracking was performed using the MTrackJ program in 4D (Meijering et al., 2012). S – spicule, Ep – epithelial cells. "
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    ABSTRACT: Sea urchin embryos sequester calcium from the sea water. This calcium is deposited in a concentrated form in granule bearing vesicles both in the epithelium and in mesenchymal cells. Here we use in vivo calcein labeling and confocal Raman spectroscopy, as well as cryo-FIB-SEM 3D structural reconstructions, to investigate the processes occurring in the internal cavity of the embryo, the blastocoel. We demonstrate that calcein stained granules are also present in the filopodial network within the blastocoel. Simultaneous fluorescence imaging and Raman spectroscopy show that these granules do contain a calcium mineral. By tracking the movements of these granules, we show that the granules in the epithelium and primary mesenchymal cells barely move, but those in the filopodial network move long distances. We could however not detect any unidirectional movement of the filopodial granules. We also show the presence of mineral containing multivesicular vesicles that also move in the filopodial network. We conclude that the filopodial network is an integral part of the mineral transport process, and possibly also for sequestering calcium and other ions. Although much of the sequestered calcium is deposited in the mineralized skeleton, a significant amount is used for other purposes, and this may be temporarily stored in these membrane-delineated intracellular deposits.
    Journal of Structural Biology 10/2015; 192(3). DOI:10.1016/j.jsb.2015.09.017 · 3.23 Impact Factor
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    • "Average line intensity profiles were made in Matlab (Meijering et al., 2012). For figures and movies, contrast enhancement, noise reduction and pseudocolouring were performed using a combination of Volocity, Photoshop and Matlab. "
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    ABSTRACT: The mature vertebrate retina is a highly ordered neuronal network of cell bodies and synaptic neuropils arranged in distinct layers. Little, however, is known about the emergence of this spatial arrangement. Here, we investigate how the three main types of retinal inhibitory neuron (RIN) - horizontal cells (HCs), inner nuclear layer amacrine cells (iACs), and displaced amacrine cells (dACs) - reach their specific laminar positions during development. Using in vivo time-lapse imaging of zebrafish retinas, we show that RINs undergo distinct phases of migration. The first phase, common to all RINs, is bipolar migration directed towards the apicobasal center of the retina. All RINs then transition to a less directionally persistent multipolar phase of migration. Finally, HCs, iACs and dACs each undergo cell-type specific migration. In contrast to current hypotheses, we find that most dACs send processes into the forming inner plexiform layer (IPL) before migrating through it and inverting their polarity. By imaging and quantifying the dynamics of HCs, iACs and dACs from birth to final position, this study thus provides evidence for distinct and new migration patterns during retinal lamination and insights into the initiation of IPL formation. © 2015. Published by The Company of Biologists Ltd.
    Development 06/2015; 142(15). DOI:10.1242/dev.122473 · 6.46 Impact Factor
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