A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.

Real-Time Adaptive Multi-Classifier Multi-Resolution Visual Tracking Framework for Unmanned Aerial Vehicles

This paper presents a novel robust visual tracking framework, based on discriminative method, for Unmanned Aerial Vehicles (UAVs) to track an arbitrary 2D/3D target at real-time frame rates, that is called the Adaptive Multi-Classifier Multi-Resolution (AMCMR) framework. In this framework, adaptive Multiple Classifiers (MC) are updated in the (k-1)th frame-based Multiple Resolutions (MR) structure with compressed positive and negative samples, and then applied them in the kth frame-based Multiple Resolutions (MR) structure to detect the current target. The sample importance has been integrated into this framework to improve the tracking stability and accuracy. The performance of this framework was evaluated with the Ground Truth (GT) in different types of public image databases and real flight-based aerial image datasets firstly, then the framework has been applied in the UAV to inspect the Offshore Floating Platform (OFP). The evaluation and application results show that this framework is more robust, efficient and accurate against the existing state-of-art trackers, overcoming the problems generated by the challenging situations such as obvious appearance change, variant illumination, partial/full target occlusion, blur motion, rapid pose variation and onboard mechanical vibration, among others. To our best knowledge, this is the first work to present this framework for solving the online learning and tracking freewill 2D/3D target problems, and applied it in the UAVs.