Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay.

International audienceBACKGROUND: The combination of time-lapse imaging of live cells with high-throughput perturbation assays is a powerful tool for genetics and cell biology. The Mitocheck project employed this technique to associate thousands of genes with transient biological phenotypes in cell division, cell death and migration. The original analysis of these data proceeded by assigning nuclear morphologies to cells at each time-point using automated image classification, followed by description of population frequencies and temporal distribution of cellular states through event-order maps. One of the choices made by that analysis was not to rely on temporal tracking of the individual cells, due to the relatively low image sampling frequency, and to focus on effects that could be discerned from population-levelbehaviour. RESULTS: Here, we present a variation of this approach that employs explicit modelling by dynamic differential equations of the cellular state populations. Model fitting to the time course data allowed reliable estimation of the penetrance and time of appearance of four types of disruption of the cell cycle: quiescence, mitotic arrest, polynucleation and cell death. Model parameters yielded estimates of the duration of the interphase and mitosis phases. We identified 2190 siRNAs that induced a disruption of the cell cycle at reproducible times, or increased the durations of the interphase or mitosis phases. CONCLUSIONS: We quantified the dynamic effects of the siRNAs and compiled them as a resource that can be used to characterize the role of their target genes in cell death, mitosis and cell cycle regulation. The described population-based modelling method might be applicable to other large-scale cell-based assays with temporal readout when only population-level measures are available

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

How to predict gene function from phenotypic cues is a longstanding question in biology.Using quantitative multiparametric imaging, RNAi-mediated cell phenotypes were measured on a genome-wide scale.On the basis of phenotypic ‘neighbourhoods', we identified previously uncharacterized human genes as mediators of the DNA damage response pathway and the maintenance of genomic integrity.The phenotypic map is provided as an online resource at http://www.cellmorph.org for discovering further functional relationships for a broad spectrum of biological modul

Video Coding with Flexible MCTF Structures for Low End-to-End Delay

Some of the most powerful schemes for scalable video coding are based on the so-called (t + 2D) paradigm and provide coding performance competitive with state-of-the-art codecs. However, the temporal multiresolution schemes used in such codecs introduce a non-negligible delay, preventing their use in applications which require low latency, like video conferencing or video streaming. In this paper, we provide a flexible approach to reduce the end-to-end delay involved in motion-compensated temporal filtering schemes. We show by simulations results the trade-offs observed between coding efficiency and low end-to-end delay

License LGPL-2.1 biocViews CellBasedAssays, Visualization, Preprocessing Suggests MASS

Description imageHTS is an R package dedicated to the analysis of high-throughput microscopybased screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopybased datasets

Optimized Prediction of Uncovered Areas in Subband Video Coding

Motion-compensated temporal filtering is an essential ingredient of recently developed wavelet-based scalable video coding schemes. Lifting implementation of these decompositions represents a versatile tool for spatio-temporal optimizations and numerous improvements have thus been proposed. In this paper, we propose an optimized prediction scheme built on a 5/3 motion-compensated filterbank but using motion vector fields in the same direction. Optimization is done by estimating one of the motion vector field such that to minimize the detail subband energy, knowing that some parts of a current image have already been predicted by the other motion vector field. Experimental results show that significant improvements in compression performance can be achieved using this strategy, for equivalent complexity. 1

Four-Band Linear-Phase Orthogonal Spatial Filter Bank for Subband Video Coding

In wavelet-based scalable video coding schemes, temporal interframe redundancy is exploited by applying a temporal wavelet transform along the motion trajectories. A spatial decomposition of the temporal subbands is further performed to take advantage of the spatial redundancy of the filtered frames. However, most of the t + 2D video codecs do not take into account the very different spatial characteristics of the temporal subband frames and use indifferently the same spatial 9/7 biorthogonal transform to decompose them. In this paper, we present a spatial transform based on a four-band filter bank, whose frequency selectivity properties are shown to be more suited to represent detail frames. We give the analytical form of a linear-phase, orthogonal and regular four-band filter bank and we show by experimental results conducted on video sequences that significant improvements in terms of PSNR can be obtained using the proposed filter bank to decompose the detail frames