CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images.

SUMMARY: Recent advances of long-term time-lapse microscopy have made it easy for researchers to quantify cell behavior and molecular dynamics at single-cell resolution. However, the lack of easy-to-use software tools optimized for customized research is still a major challenge for quantitatively understanding biological processes through microscopy images. Here, we present CellTracker, a highly integrated graphical user interface software, for automated cell segmentation and tracking of time-lapse microscopy images. It covers essential steps in image analysis including project management, image pre-processing, cell segmentation, cell tracking, manually correction and statistical analysis such as the quantification of cell size and fluorescence intensity, etc. Furthermore, CellTracker provides an annotation tool and supports model training from scratch, thus proposing a flexible and scalable solution for customized dataset analysis. AVAILABILITY AND IMPLEMENTATION: CellTracker is an open-source software under the GPL-3.0 license. It is implemented in Python and provides an easy-to-use graphical user interface. The source code, instruction manual and demos can be found at https://github.com/WangLabTHU/CellTracker. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

3D numerical study of tumor microenvironmental flow in response to vascular-disrupting treatments.

The effects of vascular-disrupting treatments on normalization of tumor microvasculature and its microenvironmental flow were investigated, by mathematical modeling and numerical simulation of tumor vascular-disrupting and tumor haemodynamics. Four disrupting approaches were designed according to the abnormal characteristics of tumor microvasculature compared with the normal one. The results predict that the vascular-disrupting therapies could improve tumor microenvironment, eliminate drug barrier and inhibit metastasis of tumor cells to some extent. Disrupting certain types of vessels may get better effects. In this study, the flow condition on the networks with "vascular-disrupting according to flowrate" is the best comparing with the other three groups, and disrupting vessels of lower maturity could effectively enhance fluid transport across vasculature into interstitial space.

Coupled modelling of tumour angiogenesis, tumour growth and blood perfusion.

We propose a mathematical modelling system to investigate the dynamic process of tumour cell proliferation, death and tumour angiogenesis by fully coupling the vessel growth, tumour growth and blood perfusion. Tumour growth and angiogenesis are coupled by the chemical microenvironment and the cell-matrix interaction. The haemodynamic calculation is carried out on the updated vasculature. The domains of intravascular, transcapillary and interstitial fluid flow were coupled in the model to provide a comprehensive solution of blood perfusion variables. An estimation of vessel collapse is made according to the wall shear stress criterion to provide feedback on vasculature remodelling. The simulation can show the process of tumour angiogenesis and the spatial distribution of tumour cells for periods of up to 24 days. It can show the major features of tumour and tumour microvasculature during the period such as the formation of a large necrotic core in the tumour centre with few functional vessels passing through, and a well circulated tumour periphery regions in which the microvascular density is high and associated with more aggressive proliferating cells of the growing tumour which are all consistent with physiological observations. The study also demonstrated that the simulation results are not dependent on the initial tumour and networks, which further confirms the application of the coupled model feedback mechanisms. The model enables us to examine the interactions between angiogenesis and tumour growth, and to study the dynamic response of a solid tumour to the changes in the microenvironment. This simulation framework can be a foundation for further applications such as drug delivery and anti-angiogenic therapies.

A haemodynamic model for heart-mural coronary artery-myocardial bridge.

An experimental model for heart-mural coronary artery-myocardial bridge was established based on the theory of haemodynamics. The application of the model demonstrated that it can repeat to great extent the phenomenon of the myocardial bridge compressing the mural coronary artery, which results in abnormal haemodynamic characteristics. The results of simulation experiments are mostly consistent with clinical research.

Study of tumor blood perfusion and its variation due to vascular normalization by anti-angiogenic therapy based on 3D angiogenic microvasculature.

The coupling of intravascular and interstitial flow is a distinct feature of tumor microcirculation, due to high vessel permeability, low osmotic pressure gradient and absence of functional lymphatic system inside tumors. We have previously studied the tumor microcirculation by using a 2D coupled model. In this paper, we extend it to a 3D case with some new considerations, to investigate tumor blood perfusion on a more realist microvasculature, and the effects of vascular normalization by anti-angiogenic therapy on tumor microenvironment. The model predict the abnormal tumor microcirculation and the resultant hostile microenvironment: (1) in the intra-tumoral vessels, blood flows slowly with almost constant pressure values, haematocrit is much lower which contributes to hypoxia and necrosis formation of the tumor centre; (2) the total transvascular flux is at the same order of magnitude as intravascular flux, the intravasation appears inside of the tumor, the ratio of the total amount of intravasation flux to extravasation flux is about 16% for the present model; (3) the interstitial pressure is uniformly high throughout the tumor and drops precipitously at the periphery, which leads to an extremely slow interstitial flow inside the tumor, and a rapidly rising convective flow oozing out from the tumor margin into the surrounding normal tissue. The investigation of the sensitivity of flows to changes in transport properties of vessels and interstitium as well as the vascular density of the vasculature, gains an insight into how normalization of tumor microenvironment by anti-angiogenic therapies influences the blood perfusion.

Coupled modeling of blood perfusion in intravascular, interstitial spaces in tumor microvasculature.

The coupling of intravascular and interstitial flow is a distinct feature of tumor microcirculation, due to the high vessel permeability, the low osmotic pressure gradient as well as the absence of functional lymphatic system inside tumors. In this paper, a coupled mathematical model of tumor microcirculation is developed, which provides the link between microvasculature and interstitial space perfusion through the matrices determining a neighbor point belonging to either connected vessel (matrix B) or interstitial space (matrix A), and combines the intravascular and interstitial flow by vascular leaky terms. In addition, the compliance of tumor vessels, blood rheology with hematocritic distribution at branches is also considered. The microvascular network, on which the microcirculation calculation is carried out, is generated from our two-dimensional 9-point (2D9P) model of tumor angiogenesis, improved from the previous 2D5P one. A specific coupling procedure is developed in the study to couple the intravascular and interstitial flow. It is based on the iteratively numerical simulation techniques, including local iterations at individual parameter level and one global loop to provide coupling and simulation convergence. The simulation results not only present the basic features and characteristics of tumor microcirculation, which agree with the corresponding experimental observations reported, but also predict an intimate relationship between the tumor intravascular and interstitial flow quantitatively. Among the parameters, the vascular leakiness is a key to govern the systemic flowing pattern, influence the tumor internal environment and contribute to the metastasis of tumor cells, which could not be presented by the previous uncoupled models.

[Pulse pressure and mean pressure relationship of intracranial pressure and lumbar cerebrospinal fluid pressure].

Intracranial pressure fluctuates due to heart beat, respiration, neuro-regulation, etc. Traditional intracranial pressure study focuses on the static pressure and related factors, putting emphasis on mean intracranial pressure, while paying little attention to the pulse components. This study was composed of two parts: animal experiment and theoretical analysis. The animal experiment was performed on 14 mongrel dogs, studying the variation of intracranial pressure wave form under different intracranial pressure level. The dogs were installed epidurally with latex sacculus to establish models of increased intracranial pressure. The degree of intracranial pressure and volume could be altered by changing the volume of fluid in the sacculus. During the process, pressure transducers were arranged to monitor and record the variations of the pressure of intracranial ventricle and lumbar subarachnoid cavity. The result demonstrated that, with the continual increase of intracranial pressure, intracranial pulse pressure increased correspondingly, showing a linear relationship with the change of intracranial pressure. After the sacculus was emptied and reinfused, the slope of the linear relationship was determined to be greater than the former slope. The same result was obtained in the lumbar cerebrospinal fluid pressure. Therefore, the lumbar cerebrospinal fluid pressure is consistent with the intracranial pressure. Intracranial pulse pressure is in linear relationship with mean pressure, and the slope of their linear relationship predicts the perform of intracranial autoregulation.

[Capillary blood flow with dynamical change of tissue pressure caused by exterior force].

A hemodynamic model of capillary and tissue, in which tissue pressure changed with swing manipulation of Traditional Chinese Medical Massage (TCMM), is presented in this paper to explain the hemodynamic mechanism of swing manipulation. Blood flowed in capillary with low Reynolds number. Plasma exuded through capillary according to the Starling's Law. Tissue pressure changed linearly with the massage force measured. Blood apparent viscosity, plasma protein concentration and red cell's hematocrit were taken into account. Capillary flow rate, blood apparent viscosity, filtration rate and filtration fraction with dynamical change of tissue pressure were calculated numerically, and were compared with those in static tissue pressure condition. Results showed that, dynamical change of tissue pressure led to the increase of capillary flow rate and the decrease of blood apparent viscosity, which qualitatively explained the hemodynamic mechanism of "promoting blood circulation and removing blood stasis" in swing manipulation of TCMM.

Lattice Boltzmann simulation on particle suspensions in a two-dimensional symmetric stenotic artery.

The technique of lattice Boltzmann simulation has been applied to the study of two-dimensional particle suspensions through a modeled arterial stenosis. The stenosis model consists of two-side symmetric semicirculars in a planar channel with the width of the stenosis throat larger than d and less than 2d, where d is the diameter of the particles. When only one particle is positioned off-centerline initially, the particle migrates off-centerline after passing the stenosis and the velocity at the stenosis throat is much larger than that in a flat tube. Only when two particles are positioned symmetrically to the centerline to a very high accuracy can the flow be blocked by two particles completely. A very small asymmetry will be amplified proximal to the stenosis throat in that one of the particles goes back to leave space to let the other particle passing the stenosis first so that the particles cannot be blocked. An evidence of attractive interactions between the particles as well as a particle and a proximal protuberance is observed when the asymmetry is very small and the width at the stenosis throat is between two critical values. The hematocrit distribution of the particles is studied by simulating multiparticle suspensions. It is found that the width of the stenosis throat has a significant influence on the hematocrit distribution of the particles in the flat tubes far from the stenosis.