Digital refocusing and extended depth of field reconstruction in Fourier ptychographic microscopy

Fourier ptychography microscopy (FPM) is a recently developed microscopic imaging method that allows the recovery of a high-resolution complex image by combining a sequence of bright and darkfield images acquired under inclined illumination. The capacity of FPM for high resolution imaging at low magnification makes it particularly attractive for applications in digital pathology which require imaging of large specimens such as tissue sections and blood films. To date most applications of FPM have been limited to imaging thin samples, simplifying both image reconstruction and analysis. In this work we show that, for samples of intermediate thickness (defined here as less than the depth of field of a raw captured image), numerical propagation of the reconstructed complex field allows effective digital refocusing of FPM images. The results are validated by comparison against images obtained with an equivalent high numerical aperture objective lens. We find that post reconstruction refocusing (PRR) yields images comparable in quality to adding a defocus term to the pupil function within the reconstruction algorithm, while reducing computing time by several orders of magnitude. We apply PRR to visualize FPM images of Giemsa-stained peripheral blood films and present a novel image processing pipeline to construct an effective extended depth of field image which optimally displays the 3D sample structure in a 2D image. We also show how digital refocusing allows effective correction of the chromatic focus shifts inherent to the low magnification objective lenses used in FPM setups, improving the overall quality of color FPM images

Data-driven malaria prevalence prediction in large densely populated urban holoendemic sub-Saharan West Africa

Over 200 million malaria cases globally lead to half-million deaths annually. The development of malaria prevalence prediction systems to support malaria care pathways has been hindered by lack of data, a tendency towards universal "monolithic" models (one-size-fits-all-regions) and a focus on long lead time predictions. Current systems do not provide short-term local predictions at an accuracy suitable for deployment in clinical practice. Here we show a data-driven approach that reliably produces one-month-ahead prevalence prediction within a densely populated all-year-round malaria metropolis of over 3.5 million inhabitants situated in Nigeria which has one of the largest global burdens of P. falciparum malaria. We estimate one-month-ahead prevalence in a unique 22-years prospective regional dataset of > 9 × 10^{4} participants attending our healthcare services. Our system agrees with both magnitude and direction of the prediction on validation data achieving MAE ≤ 6 × 10^{-2}, MSE ≤ 7 × 10^{-3}, PCC (median 0.63, IQR 0.3) and with more than 80% of estimates within a (+ 0.1 to - 0.05) error-tolerance range which is clinically relevant for decision-support in our holoendemic setting. Our data-driven approach could facilitate healthcare systems to harness their own data to support local malaria care pathways

Worker Flows in the European Union During the Great Recession

We measure the contribution of worker flows across employment, unemployment, and non-participation to the change in unemployment in eleven EU countries during the period 2006-2012, paying special attention to which socio-demographic groups in each of the countries were mostly affected by job creation and job destruction during the crisis. We find that age, to a larger extent than educational attainments, is the main determinant of flows from employment into unemployment, particularly in those countries where unemployment increased by most. Secondly, we highlight some institutional features of the labour market (employment protection legislation, unemployment insurance, and the incidence of active labor market policies) that help to explain the cross-country differences in flows between employment and unemployment and in their socio-demographic composition. Finally, we examine if the crisis has led to some employment reallocation across sectors, finding that, so far, there is no clear evidence in favor of cleansing effects

De nouvelles stratégies pour l'allocation des coûts de congestion sur une base physique

International audienc

Three years after transplants in human mandibles, histological and in-line HT revealed that stem cells regenerated a compact rather than a spongy bone: biological and clinical implication

International audienceMesenchymal stem cells deriving from dental pulp differentiate into osteoblasts capable of producing bone. In previous studies, we extensively demonstrated that, when seeded on collagen I scaffolds, these cells can be conveniently used for the repair of human mandible defects. Here, we assess the stability and quality of the regenerated bone and vessel network 3 years after the grafting intervention, with conventional procedures and in-line holotomography, an advanced phase-imaging method using synchrotron radiation that offers improved sensitivity toward low-absorbing structures. We found that the regenerated tissue from the graft sites was composed of a fully compact bone with a higher matrix density than control human alveolar spongy bone from the same patient. Thus, the regenerated bone, being entirely compact, is completely different from normal alveolar bone. Although the bone regenerated at the graft sites is not of the proper type found in the mandible, it does seem to have a positive clinical impact. In fact, it creates steadier mandibles, may well increase implant stability, and, additionally, may improve resistance to mechanical, physical, chemical, and pharmacological agents