The spread of infectious diseases such as COVID-19 presents many challenges to healthcare systems and infrastructures across the world, exacerbating inequalities and leaving the world's most vulnerable populations most affected. Given their density and available infrastructure, refugee and internally displaced person (IDP) settlements can be particularly susceptible to disease spread. In this paper we present an agent-based modeling approach to simulating the spread of disease in refugee and IDP settlements under various non-pharmaceutical intervention strategies. The model, based on the June open-source framework, is informed by data on geography, demographics, comorbidities, physical infrastructure and other parameters obtained from real-world observations and previous literature. The development and testing of this approach focuses on the Cox's Bazar refugee settlement in Bangladesh, although our model is designed to be generalizable to other informal settings. Our findings suggest the encouraging self-isolation at home of mild to severe symptomatic patients, as opposed to the isolation of all positive cases in purpose-built isolation and treatment centers, does not increase the risk of secondary infection meaning the centers can be used to provide hospital support to the most intense cases of COVID-19. Secondly we find that mask wearing in all indoor communal areas can be effective at dampening viral spread, even with low mask efficacy and compliance rates. Finally, we model the effects of reopening learning centers in the settlement under various mitigation strategies. For example, a combination of mask wearing in the classroom, halving attendance regularity to enable physical distancing, and better ventilation can almost completely mitigate the increased risk of infection which keeping the learning centers open may cause. These modeling efforts are being incorporated into decision making processes to inform future planning, and further exercises should be carried out in similar geographies to help protect those most vulnerable.

Humanitarian response to natural disasters and conflicts can be assisted by satellite image analysis. In a humanitarian context, very specific satellite image analysis tasks must be done accurately and in a timely manner to provide operational support. We present PulseSatellite, a collaborative satellite image analysis tool which leverages neural network models that can be retrained on-the fly and adapted to specific humanitarian contexts and geographies. We present two case studies, in mapping shelters and floods respectively, that illustrate the capabilities of PulseSatellite.

COVID-19, the disease caused by the SARS-CoV-2 virus, has been declared a pandemic by the World Health Organization, which has reported over 18 million confirmed cases as of August 5, 2020. In this review, we present an overview of recent studies using Machine Learning and, more broadly, Artificial Intelligence, to tackle many aspects of the COVID19 crisis. We have identified applications that address challenges posed by COVID-19 at different scales, including: molecular, by identifying new or existing drugs for treatment; clinical, by supporting diagnosis and evaluating prognosis based on medical imaging and non-invasive measures; and societal, by tracking both the epidemic and the accompanying infodemic using multiple data sources. We also review datasets, tools, and resources needed to facilitate Artificial Intelligence research, and discuss strategic considerations related to the operational implementation of multidisciplinary partnerships and open science. We highlight the need for international cooperation to maximize the potential of AI in this and future pandemics.

The Mediterranean Sea is the stage of one of the biggest humanitarian crises to affect Europe. Since 2014, thousands of migrants and refugees have died or gone missing in dangerous attempts to cross into the continent. However, there is relatively little structured information available on how they attempt the crossing. Such information could be used to better target maritime rescue efforts or to anticipate smuggling patterns, which could potentially save lives. In this article, we provide an overview of data sources available for the study of migration in the Central Mediterranean. We describe how these data can be structured, combined, and analyzed to provide quantitative insights on the situation in the region. We define a quantified rescue framework for fusing different data sources around individual rescue operations, and we explore the potential of machine learning to perform automated rescue detection based on vessel trajectory information. We conclude with technical research questions, and potential policy and operational implications related to the use of these data sources.

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.

MOTIVATION: Multi-view microscopy techniques such as Light-Sheet Fluorescence Microscopy (LSFM) are powerful tools for 3D + time studies of live embryos in developmental biology. The sample is imaged from several points of view, acquiring a set of 3D views that are then combined or fused in order to overcome their individual limitations. Views fusion is still an open problem despite recent contributions in the field. RESULTS: We developed a wavelet-based multi-view fusion method that, due to wavelet decomposition properties, is able to combine the complementary directional information from all available views into a single volume. Our method is demonstrated on LSFM acquisitions from live sea urchin and zebrafish embryos. The fusion results show improved overall contrast and details when compared with any of the acquired volumes. The proposed method does not need knowledge of the system's point spread function (PSF) and performs better than other existing PSF independent fusion methods. AVAILABILITY AND IMPLEMENTATION: The described method was implemented in Matlab (The Mathworks, Inc., USA) and a graphic user interface was developed in Java. The software, together with two sample datasets, is available at http://www.die.upm.es/im/software/SPIMFusionGUI.zip A public release, free of charge for non-commercial use, is planned after the publication of this article.

We propose to directly process 3D + t image sequences with mathematical morphology operators using a new classification of the 3D+t structuring elements. Several methods (filtering, tracking, segmentation) dedicated to the analysis of 3D + t datasets of zebrafish embryogenesis are introduced and validated through a synthetic dataset. Then, we illustrate the application of these methods to the analysis of datasets of zebrafish early development acquired with various microscopy techniques. This processing paradigm produces spatio-temporal coherent results as it benefits from the intrinsic redundancy of the temporal dimension and minimizes the needs for human intervention in semi-automatic algorithms.

Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.

We propose in this paper to perform mathematical morphology operators in a geometric transformation of an image. As a result of this procedure, processing images with regular structuring elements in the transformed domain is equivalent to working with deformed structuring elements in the original representation. More specifically, the conversion into polar-logarithmic coordinates provides satisfying results in image analysis applied to round objects, if they are roughly origin-centered. We have illustrated the interest of the derived cyclic morphology with two pattern recognition examples: erythrocyte shape analysis and multiscale description of iris textures.

We propose an extension of the classical morphological filtering based on openings by line segment structuring elements. It consists in filtering a 3D+time image with the opening by all the possible rotations of a segment in the 4D space, given an initial segment and a rotation angle. The method has been applied to remove noise from confocal laser scanning microscopy images of live zebrafish embryos engineered to fluorescently label all their cell membranes.