On the Quantification of Cellular Velocity Fields

Vig, Dhruv K.; Hamby, Alex; Wolgemuth, Charles W.

doi:10.1016/j.bpj.2016.02.032

Cited by 67 publications

(88 citation statements)

References 31 publications

(49 reference statements)

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“…The sample pixel size defines the dynamic resolution of the results independently of its dimensions (here down to 65 nm). We use Optical Flow (OF) to estimate the direction and amplitude of the motion of fluorescent labeled DNA and histones over a 30 second time interval at 5 fps, and confirm that an OF formulation is more sensitive than PIV for studying the motion of intracellular objects (25). We calculate the spatial and temporal correlation based on both direction and amplitude of each displacement vector, and quantify characteristic length scales of correlated motion with nano-scale resolution.…”

Section: Introductionmentioning

confidence: 74%

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

Shaban¹,

Barth²,

Bystricky³

2017

Preprint

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Intrinsic dynamics of chromatin contribute to gene regulation. How chromatin mobility responds to genomic processes and whether this response relies on coordinated movement is still unclear. Here, CC-BY-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/230789 doi: bioRxiv preprint first posted online Dec. 7, 2017; Significance StatementControl of gene expression relies on modifications of chromatin structure and activity of the transcription machinery. However, how chromatin responds dynamically to this genomic process and whether this response is coordinated in space is still unclear. We introduce a novel approach called Dense Flow reConstruction and Correlation (DFCC) to characterize spatially correlated dynamics of chromatin in living cells at nanoscale resolution. DFCC allows us to detect chromatin domains in living cells with long range correlations over the entire nucleus. Furthermore, transitions between domains can be quantified by the newly introduced smoothness parameter of local chromatin motion. The DFCC approach permits characterizing stochastically forming domains of other DNA dependent activity in any cell type in real time imaging.

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Section: Introductionmentioning

confidence: 74%

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

Shaban¹,

Barth²,

Bystricky³

2017

Preprint

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“…Cellular motion was measured with particle image velocimetry for monolayers (Thielicke and Stamhuis, 2014) and optical flow for Drosophila (Vig et al ., 2016). Mean cell radius was computed for each field of view using custom software to segment Hoechst 33342–stained nuclei and is defined as the radius of a circle with area equivalent to the mean cell area.…”

Section: Methodsmentioning

confidence: 99%

Cell density and actomyosin contractility control the organization of migrating collectives within an epithelium

Loza

Koride

Schimizzi

et al. 2016

MBoC

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“…Next, we investigated the migratory properties of the central mesoderm. We performed a three-dimensional optic flow analysis ; 3D-KLT, [15] in zebrafish embryos to obtain local tissue velocity measurements of both the mesoderm and ectoderm, see Methods for details. To aid quantification, we mapped the flow of the migrating tissues onto a sphere (obtained from a spherical fit of the embryo shape) and calculated velocities in spherical coordinates.…”

Section: Tip Cells Are Required To Shape the Zebrafish Notochordmentioning

confidence: 99%

Pcdh18a-positive tip cells instruct notochord formation in zebrafish

Bösze¹,

Mattes

Sinner³

et al. 2018

Preprint

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The notochord defines the axial structure of all vertebrates during development.Notogenesis is a result of major cell reorganization in the mesoderm, the convergence and the extension of the axial cells. However, it is currently not known how these processes act together in a coordinated way during notochord formation. Analysing the tissue flow, we determined the displacement of the axial mesoderm and identified, relative to the ectoderm, an actively-migrating notochord tip cell population and a group of trailing notochordal plate cells. Molecularly, these tip cells express Protocadherin18a, a member of the cadherin superfamily. We show that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms these tip cells into a cohesive and fast migrating cell group. In turn, these tip cells subsequently instruct the trailing mesoderm. We simulated cell migration during early mesoderm formation using a lattice-based mathematical framework, and predicted that the requirement for an anterior, local motile cell cluster could guide the intercalation of the posterior, axial cells. Indeed, grafting experiments validated the predictions and induced ectopic notochord-like rods. Our findings indicate that the tip cells influence the trailing mesodermal cell sheet by inducing the formation of the notochord.

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On the Quantification of Cellular Velocity Fields

Cited by 67 publications

References 31 publications

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

Cell density and actomyosin contractility control the organization of migrating collectives within an epithelium

Pcdh18a-positive tip cells instruct notochord formation in zebrafish

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