Abstract:
:We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from the centre, and is especially suitable for tracking endogeneous particles in the cell, imaged with bright field, phase contrast or fluorescence optical microscopy. Furthermore, the method can simultaneously track particles of all different sizes, and allows significant freedom in their shape. The algorithm is evaluated using the quantitative measures of accuracy and precision of previous authors, using simulated images at variable signal-to-noise ratios. To these we add new tests: the error due to a non-uniform background, and the error due to two particles approaching each other. Finally the tracking of particles in real cell images is demonstrated. The method is made freely available for non-commercial use as a software package with a graphical user-interface, which can be run within the Matlab programming environment.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Rogers SS,Waigh TA,Zhao X,Lu JRdoi
10.1088/1478-3975/4/3/008subject
Has Abstractpub_date
2007-10-09 00:00:00pages
220-7issue
3eissn
1478-3967issn
1478-3975pii
S1478-3975(07)55917-0journal_volume
4pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全abstract::Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune re...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/3/036009
更新日期:2009-05-21 00:00:00
abstract::Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abbf32
更新日期:2020-10-07 00:00:00
abstract::Branching morphogenesis is a widely spread phenomenon in nature. In organogenesis, it results from the inhomogeneous growth of the epithelial sheet, leading to its repeated branching into surrounding mesoderm. Lung morphogenesis is an emblematic example of tree-like organogenesis common to most mammals. The core signa...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/6/066006
更新日期:2012-12-01 00:00:00
abstract::Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field. ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/aa5b6a
更新日期:2017-02-16 00:00:00
abstract::We propose a reaction model for the palytoxin-sodium-potassium (PTX-Na(+)/K(+)) pump complex. The model, which is similar to the Albers-Post model for Na(+)/K(+)-ATPase, is used to elucidate the effect of PTX on Na(+)/K(+)-ATPase during the enzyme interactions with Na(+) and/or K(+) ions. Conformational substates and ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/3/036005
更新日期:2008-07-29 00:00:00
abstract::Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, under certain conditions, the large number of receptors can result in a competition among receptors to be the firs...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/035008
更新日期:2013-06-01 00:00:00
abstract::Self-organization processes in multicellular aggregates of bacteria and amoebae offer fascinating insights into the evolution of cooperation and differentiation of cells. During myxobacterial development a variety of spatio-temporal patterns emerges such as counterpropagating waves of cell density that are known as ri...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/3/2/006
更新日期:2006-06-23 00:00:00
abstract::Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation descripti...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/6/066010
更新日期:2016-12-06 00:00:00
abstract::Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane, but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/3/4/002
更新日期:2006-11-22 00:00:00
abstract::We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/4/S09
更新日期:2005-11-09 00:00:00
abstract::Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevol...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/1/016003
更新日期:2014-12-04 00:00:00
abstract::This comment argues against the view that cancer cells produce less entropy than normal cells as stated in a recent paper by Marín and Sabater. The basic principle of estimation of entropy production rate in a living cell is discussed, emphasizing the fact that entropy production depends on both the amount of heat exc...
journal_title:Physical biology
pub_type: 评论,杂志文章
doi:10.1088/1478-3975/aa8eab
更新日期:2018-02-08 00:00:00
abstract::Calcium homeostasis is considered to be one of the most important factors for the contraction and relaxation of the heart muscle. However, under some pathological conditions, such as heart failure (HF), calcium homeostasis is disordered, and spontaneous waves may occur. In this study, we developed a mathematical model...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/2/026005
更新日期:2010-05-26 00:00:00
abstract::Cancer cells are known to modify their micro-environment such that it can sustain a larger population, or, in ecological terms, they construct a niche which increases the carrying capacity of the population. It has however been argued that niche construction, which benefits all cells in the tumour, would be selected a...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/5/056001
更新日期:2015-08-12 00:00:00
abstract::Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/5/056011
更新日期:2013-10-01 00:00:00
abstract::A cluster of neural crest cells (NCCs) may chemotax up a shallow external gradient to which a single cell is unresponsive. To explain this intriguing 'group advantage', we propose a chemo-mechanical model based on the signaling proteins Rac1 and RhoA. We represent each cell as a polygon with nodes connected by elastic...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab71f1
更新日期:2020-03-10 00:00:00
abstract::By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfl...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046004
更新日期:2013-08-01 00:00:00
abstract::Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein intera...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035002
更新日期:2011-06-01 00:00:00
abstract::Monolayer expansion has generated great interest as a model system to study collective cell migration. During such an expansion the culture front often develops 'fingers', which we have recently modeled using a proposed feedback between the curvature of the monolayer's leading edge and the outward motility of the edge...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aa6591
更新日期:2017-05-03 00:00:00
abstract::Type I collagen is a versatile biomaterial that is widely used in medical applications due to its weak antigenicity, robust biocompatibility, and its ability to be modified for a wide array of applications. As such, collagen has become a major component of many tissue engineering scaffolds, drug delivery platforms, an...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/12/6/061002
更新日期:2015-12-21 00:00:00
abstract::'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/3/036002
更新日期:2010-08-11 00:00:00
abstract::Single-molecule manipulation has allowed the forced unfolding of multidomain proteins. Here we develop a theory that not only explains these experiments, but also points out a number of difficulties in their interpretation and makes suggestions for further experiments. Our theory is valid for essentially any molecule ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/2/025005
更新日期:2009-07-01 00:00:00
abstract::The one-cell amphibian embryo is modeled as a rigid spherical shell containing equal volumes of two immiscible fluids with different densities and viscosities and a surface tension between them. The fluids represent denser yolk in the bottom hemisphere and clearer cytoplasm and the germinal vesicle in the top hemisphe...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/1/015006
更新日期:2008-04-10 00:00:00
abstract::Trauma arising from landmines and improvised explosive devices promotes heterotopic ossification, the formation of extra-skeletal bone in non-osseous tissue. To date, experimental platforms that can replicate the loading parameter space relevant to improvised explosive device and landmine blast wave exposure have not ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab7d1c
更新日期:2020-08-12 00:00:00
abstract::The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological syst...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/4/045006
更新日期:2015-06-29 00:00:00
abstract::Recently, major progress has been made to develop computational models to predict and explain the mechanisms and behaviors of gene regulation. Here, we review progress on how these mechanisms and behaviors have been interpreted with analog models, where cell properties continuously modulate transcription, and digital ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/12/4/045004
更新日期:2015-06-18 00:00:00
abstract::This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary to advance biology and its applications. ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/6/063002
更新日期:2015-12-30 00:00:00
abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/045001
更新日期:2012-08-01 00:00:00
abstract::The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounte...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/1/016002
更新日期:2009-12-11 00:00:00
abstract::Chemotaxis is the process by which cells sense changes in their chemical environment and move towards more favorable conditions. In divergent species of bacteria, the chemotaxis proteins localize to the poles of the cell and information is transferred to the flagellar motors through the phosphorylation of a soluble pr...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/3/002
更新日期:2005-07-14 00:00:00