Cell motility is governed by a complex molecular machinery that converts physico-chemical cues into whole-cell movement. Understanding the underlying biophysical mechanisms requires the ability to measure physical quantities inside the cell in a simple, reproducible and preferably non-invasive manner. To this end, we developed BioFlow, a computational mechano-imaging method and associated software able to extract intracellular measurements including pressure, forces and velocity everywhere inside freely moving cells in two and three dimensions with high spatial resolution in a non-invasive manner. This is achieved by extracting the motion of intracellular material observed using fluorescence microscopy, while simultaneously inferring the parameters of a given theoretical model of the cell interior. We illustrate the power of BioFlow in the context of amoeboid cell migration, by modelling the intracellular actin bulk flow of the parasite Entamoeba histolytica using fluid dynamics, and report unique experimental measures that complement and extend both theoretical estimations and invasive experimental measures. Thanks to its flexibility, BioFlow is easily adaptable to other theoretical models of the cell, and alleviates the need for complex or invasive experimental conditions, thus constituting a powerful tool-kit for mechano-biology studies. BioFlow is open-source and freely available via the Icy software.

We study the polarization-dependent polariton-polariton interaction through its effect on a parametric scattering process in a microcavity (MC). The ratio of the anticircular interaction strength ${V}_{2}$ over its cocircular counterpart ${V}_{1}$ is involved in defining the regime in which many nonlinear processes arise in MCs, such as parametric conversion or condensation. We measure the ratio ${V}_{2}/{V}_{1}$ using a stimulated energy-degenerate parametric scattering process in a multiple MC. The sample is pumped at normal incidence, probed with a nonzero angle, and the phase-matched idler is observed at the opposite angle. The idler behavior, both in power and polarization, is compared to a Hamiltonian interaction model that takes into account the two polarization-dependent parametric scattering channels characterized by ${V}_{1}$ and ${V}_{2}$. The proposed method to measure the ratio ${V}_{2}/{V}_{1}$ is convenient and precise. The flexibility of the triple MC allows us to observe the process and measure this ratio over a large range of detunings, where we find it to be highly dependent on the detuning. These measurements complement the previous study of Vladimirova et al. [Phys. Rev. B 82, 075301 (2010)] with an original approach and for detunings that were unexplored up to now.

We propose a realistic model of cell and membrane deformations based on fluid mechanics. We focus on the blebbing process, a key mechanism of motility for several cell types. It is seen as a rupture of symmetry in the surface tension forces affecting the membrane of the cell. It produces sudden protrusions in regions where the tension forces vanish, inducing large displacements of cell material and whole-cell movement. We describe the cell and the external medium as fluids subject to Stokes equations, and the cell membrane as an interface defined by an advected level set function and subject to surface tension. We setup a numerical implementation in two dimensions using finite elements and show that the model successfully produces whole-cell movement, without involving substrate adhesion nor specific organelles. This work paves the way for further studies on the shape and dynamics of the blebs, in direct relation with live cell imaging.

We present a comprehensive investigation of optical parametric oscillation in resonantly excited one-dimensional semiconductor microcavities with embedded quantum wells. Such solid-state structures feature a fine control over light-matter coupling and produce a photonic/polaritonic mode fan that is exploited for the efficient emission of parametric beams. We implement an energy-degenerate optical parametric oscillator with balanced signal and idler intensities via a polarization-inverting mechanism. In this paper, we (i) precisely review the multimode photonic/polaritonic structure of individual emitters, (ii) provide a thorough comparison between experiment and theory, focusing on the power and the threshold dependence on the exciton-photon detuning, (iii) discuss the influence of inhomogeneous broadening of the excitonic transition and finite size, and (iv) find that a large exciton-photon detuning is a key parameter to reach a high output power and a high conversion efficiency. Our study highlights the predictive character of the polariton interaction theory and the flexibility of one-dimensional semiconductor microcavities as a platform to study parametric phenomena. DOI: 10.1103/PhysRevB.87.155302

Bioimage informatics has emerged as a new interdisciplinary research endeavor for bringing the power of computational and mathematical sciences into the biological imaging arena. We describe an open-source software platform, Icy, that proposes a comprehensive framework for easy algorithm development and deployment fostering community-oriented efforts. Icy offers a platform to share and publish collaborative algorithm developments, while promoting re-usability and code sharing to ease the development of new algorithms, and simplifying user's feedback and support through a community web site.

Received 20 January 2012DOI:https://doi.org/10.1103/PhysRevB.85.049902©2012 American Physical Society

The features of resonant secondary emission by two-dimensional multiple semiconductor microcavities are experimentally investigated. The multiband photonic/polaritonic dispersion makes possible a normal laser incidence which represents an isotropic probe of the system defectivity. We show that the static disorder determines the final states of the resonant Rayleigh scattering in the high-symmetry axes of the GaAs matrix. Scanning transmission electron microscopy and x-ray-diffraction measurements reveal the origins of disorder: a small misfit dislocation density and step formation at the layer interfaces due to strain accumulation and relaxation. These mosaicity effects ruled by the symmetry of the underlying GaAs matrix are common features of thick and strained crystals and determine the scattering channels by selecting the crystallographic discretized directions. The structural characterization demonstrates that, while the presence of misfit dislocations plays a minor role, the principal source of disorder is due to the elastic relaxation of strain. Moreover, interband optical parametric oscillation of the intensity balanced signal and idler beams is seeded by the resonant Rayleigh scattering and takes place in the directions selected by the photonic disorder in the distributed Bragg reflector.

We present an experimental investigation of parametric scattering processes and optical parametric oscillations in wire shaped, one‐dimensional semiconductor microcavities. Far field emission patterns and corresponding band dispersion are studied by polarization resolved measurements and power dependence measurements under resonant and non‐resonant excitation. The multiplicity of the photonic bands allows for an efficient engineering of interbranch parametric scattering processes. We demonstrate the onset of optical parametric oscillation of perfectly balanced twin beams, degenerate in energy and split in momentum space.

We aim at analysing fluorescence microscopy sequences of moving cells, so as to estimate the velocities that define the movement, the forces that drive this movement, and the pressure that characterises the material state. We use an optical flow method constrained by Stokes flow mechanics equations that define the dynamics of a fluid that is incompressible, homogeneous and viscous. We present a finite element formulation that leads to a quadratic programming problem. We apply the method to real biological data of amoebas observed by fluorescence microscopy.

Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.

We report on a detailed experimental investigation of interbranch parametric scattering processes in one-dimensional semiconductor microcavities. Band dispersion and corresponding far-field emission patterns are studied by polarization-resolved and power-dependence measurements under resonant and nonresonant excitation at normal incidence. We demonstrate the realization of optical parametric oscillation of balanced twin beams, which are degenerate in energy and split in momentum space. This achievement is shown for both the strong and the weak coupling regime, highlighting the versatility of this peculiar microcavity system.