Non-rigid multi-frame registration of cell nuclei in live cell microscopy image data

To gain a better understanding of cellular and molecular processes it is important to quantitatively analyze the motion of subcellular particles in live cell microscopy image sequences. For accurate quantification of the subcellular particle motion, compensation of the motion and deformation of the cell nucleus is required. This thesis deals with non-rigid registration of cell nuclei in 2D and 3D live cell fluorescence microscopy images. We developed two multi-frame non-rigid registration approaches which simultaneously exploit information from multiple consecutive frames of an image sequence to improve the registration accuracy. The multi-frame registration approaches are based on local optic flow estimation, use information from multiple consecutive images, and take into account computed transformations from previous time steps. The first approach comprises three intensity-based variants and two different temporal weighting schemes. The second approach determines diffeomorphic transformations in the log-domain which allows efficient computation of the inverse transformations. We use a temporally weighted mean image which is constructed based on inverse transformations and multiple consecutive frames. In addition, we employ a flow boundary preserving method for regularization of computed deformation vector fields. Both multi-frame registration approaches have been successfully applied to 2D and 3D synthetic as well as real live cell microscopy image sequences. We have performed an extensive quantitative evaluation of our approaches and compared their performance with previous non-rigid pairwise, multi-frame, and temporal groupwise registration approaches

Non-rigid Contour-Based Registration of Cell Nuclei in 2D Live Cell Microscopy Images Using a Dynamic Elasticity Model

International audienceThe analysis of the pure motion of subnuclear structures without influence of the cell nucleus motion and deformation is essential in live cell imaging. In this work, we propose a 2D contour-based image registration approach for compensation of nucleus motion and deformation in fluorescence microscopy time-lapse sequences. The proposed approach extends our previous approach which uses a static elasticity model to register cell images. Compared to that scheme, the new approach employs a dynamic elasticity model for forward simulation of nucleus motion and deformation based on the motion of its contours. The contour matching process is embedded as a constraint into the system of equations describing the elastic behavior of the nucleus. This results in better performance in terms of the registration accuracy. Our approach was successfully applied to real live cell microscopy image sequences of different types of cells including image data that was specifically designed and acquired for evaluation of cell image registration methods. An experimental comparison with existing contour-based registration methods and an intensity-based registration method has been performed. We also studied the dependence of the results on the choice of method parameters

Color Consistency and Local Contrast Enhancement for a Mobile Image-Based Change Detection System

Mobile change detection systems allow for acquiring image sequences on a route of interest at different time points and display changes on a monitor. For the display of color images, a processing approach is required to enhance details, to reduce lightness/color inconsistencies along each image sequence as well as between corresponding image sequences due to the different illumination conditions, and to determine colors with natural appearance. We have developed a real-time local/global color processing approach for local contrast enhancement and lightness/color consistency, which processes images of the different sequences independently. Our approach combines the center/surround Retinex model and the Gray World hypothesis using a nonlinear color processing function. We propose an extended gain/offset scheme for Retinex to reduce the halo effect on shadow boundaries, and we employ stacked integral images (SII) for efficient Gaussian convolution. By applying the gain/offset function before the color processing function, we avoid color inversion issues, compared to the original scheme. Our combined Retinex/Gray World approach has been successfully applied to pairs of image sequences acquired on outdoor routes for change detection, and an experimental comparison with previous Retinex-based approaches has been carried out

Introduction aux automates cellulaires de type " lattice-gas ". Application à la croissance in vitro des gliomes et à l'identification de leurs mécanismes d'invasion

National audienc

Non-Rigid Multi-Frame registration of cell nuclei in live cell fluorescence microscopy image data

The analysis of the motion of subcellular particles in live cell microscopy images is essential for understanding biological processes within cells. For accurate quantification of the particle motion, compensation of the motion and deformation of the cell nucleus is required. We introduce a non-rigid multi-frame registration approach for live cell fluorescence microscopy image data. Compared to existing approaches using pairwise registration, our approach exploits information from multiple consecutive images simultaneously to improve the registration accuracy. We present three intensity-based variants of the multi-frame registration approach and we investigate two different temporal weighting schemes. The approach has been successfully applied to synthetic and live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise registration has been carried out

Herpesviral Replication Compartments Move and Coalesce at Nuclear Speckles to Enhance Export of Viral Late mRNA

The role of the intranuclear movement of chromatin in gene expression is not well understood. Herpes simplex virus forms replication compartments (RCs) in infected cell nuclei as sites of viral DNA replication and late gene transcription. These structures develop from small compartments that grow in size, move and coalesce. Quantitative analysis of RC trajectories, derived from 4D images, show that most RCs move by directed motion. Directed movement is impaired in the presence of actin and myosin inhibitors as well as a transcription inhibitor. In addition, RCs coalesce at and reorganize nuclear speckles. Lastly, distinct effects of actin and myosin inhibitors on viral gene expression suggest that RC movement is not required for transcription but rather, movement results in the bridging of transcriptionally active RCs with nuclear speckles to form structures that enhance export of viral late mRNAs