Structure-dependent amplification for denoising and background correction in Fourier ptychographic microscopy

Fourier Ptychographic Microscopy (FPM) allows high resolution imaging using iterative phase retrieval to recover an estimate of the complex object from a series of images captured under oblique illumination. FPM is particularly sensitive to noise and uncorrected background signals as it relies on combining information from brightfield and noisy darkfield (DF) images. In this article we consider the impact of different noise sources in FPM and show that inadequate removal of the DF background signal and associated noise are the predominant cause of artefacts in reconstructed images. We propose a simple solution to FPM background correction and denoising that outperforms existing methods in terms of image quality, speed and simplicity, whilst maintaining high spatial resolution and sharpness of the reconstructed image. Our method takes advantage of the data redundancy in real space within the acquired dataset to boost the signal-to-background ratio in the captured DF images, before optimally suppressing background signal. By incorporating differentially denoised images within the classic FPM iterative phase retrieval algorithm, we show that it is possible to achieve efficient removal of background artefacts without suppression of high frequency information. The method is tested using simulated data and experimental images of thin blood films, bone marrow and liver tissue sections. Our approach is non-parametric, requires no prior knowledge of the noise distribution and can be directly applied to other hardware platforms and reconstruction algorithms making it widely applicable in FPM

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

Uprolides N, O and P from the Panamanian Octocoral Eunicea succinea.

Three new diterpenes, uprolide N (1), uprolide O (2), uprolide P (3) and a known one, dolabellane (4), were isolated from the CH₂Cl₂-MeOH extract of the gorgonian octocoral Eunicea succinea, collected from Bocas del Toro, on the Caribbean coast of Panama. Their structures were determined using spectroscopic analyses, including 1D and 2D NMR and high-resolution mass spectrometry (HRMS) together with molecular modeling studies. Compounds 1-3 displayed anti-inflammatory properties by inhibiting production of Tumor Necrosis Factor (TNF) and Interleukin (IL)-6 induced by lipopolysaccharide (LPS) in murine macrophages

Fusion of SPOT5 multispectral and Ikonos panchromatic images

International audienceThe offer of high spectral and high spatial resolutions images has grown in the last decade. It is know possible to obtain data from different sources with different spatial and spec-tral resolutions. The field of data fusion of remotely sensed data grown also very fast in the last years. In this paper, an algorithm allowing the merging of SPOT 5 images and Ikonos images are proposed. This algorithm is based on the ARSIS concept and presents an implementation for a ratio of spatial resolution equal to 10. The ARSIS concept is first detailed. Then, the way of de-fining a new implementation based on this concept is presented, allowing to understand how to define new implementations and to develop new solutions based on this concept. The proposed algorithm is developed, describing the different steps for building a fused product from a SPOT 5 multispectral data at 10 m and from a IKONOS panchromatic data at 1 m. Some other methods are proposed. The evaluation of the quality of the different methods is achieved using a set of quantitative quality parameters. The visual quality of the products are evaluated by a set of inter-preters. Conclusions are drawn on the quality of the proposed products

Achilles Tendon and Athletes

Achilles tendon (AT) is the strongest human tendon. AT disorders are common among athletes. AT pathologies vary from tendinopathy to frank rupture. Diagnosis is made clinically. Imaging modalities are used adjunctively. Management of AT rupture in athletes is challenging to surgeons due to worldwide growing popularity of sports and potential social and financial impact of AT injury to an athlete. Hence, new surgical techniques aim at attaining quick recovery with good outcome, finding similar results with both open and percutaneous techniques when accompanying these with functional rehabilitation protocols. Non-operative strategies include shoe wear modification, physiotherapy and extracorporeal shock wave therapy. Surgical interventions vary based on the AT pathology nature and extent. Direct repair can work for small-sized defects. V-Y gastrocnemius advancement could approximate the tendon edges for repair within 2–8 cm original gap. Gastrocnemius turndown can bridge tendon loss > 8 cm. Autogenous, allogeneous or synthetic tendon grafts were used for AT reconstruction purposes. In AT tendinopathies with no tendon tissue loss, surgical procedures revolve around induction of tissue repair through lesion incision or debridement to full detachment followed by reattachment. Extra-precautions are exercised for prevention of AT disorders especially among susceptible athletes participating in sports involving excessive AT strain

Optical mesoscopy, machine learning and computational microscopy enable high information content diagnostic imaging of blood films

Automated image-based assessment of blood films has tremendous potential to support clinical haematology within overstretched healthcare systems. To achieve this, efficient and reliable digital capture of the rich diagnostic information contained within a blood film is a critical first step. However, this is often challenging, and in many cases entirely unfeasible, with the microscopes typically used in haematology due to the fundamental trade-off between magnification and spatial resolution. To address this, we investigated three state-of-the-art approaches to microscopic imaging of blood films which leverage recent advances in optical and computational imaging and analysis to increase the information capture capacity of the optical microscope: optical mesoscopy, which uses a giant microscope objective (Mesolens) to enable high resolution imaging at low magnification; Fourier ptychographic microscopy, a computational imaging method which relies on oblique illumination with a series of LEDs to capture high resolution information; and deep neural networks which can be trained to increase the quality of low magnification, low resolution images. We compare and contrast the performance of these techniques for blood film imaging for the exemplar case of Giemsa-stained peripheral blood smears. Using computational image analysis and shape-based object classification we demonstrate their use for automated analysis of red blood cell morphology and visualization and detection of small blood borne parasites such as the malarial parasite Plasmodium falciparum. Our results demonstrate that these new methods greatly increase the information capturing capacity of the light microscope with transformative potential for haematology and more generally across digital pathology. This article is protected by copyright. All rights reserved

Donated human milk as a determinant factor for the gut bifidobacterial ecology in premature babies

Correct establishment of the gut microbiome is compromised in premature babies, with Bifidobacterium being one of the most affected genera. Prematurity often entails the inability to successfully breastfeed, therefore requiring the implementation of other feeding modes; breast milk expression from a donor mother is the recommended option when their own mother’s milk is not available. Some studies showed different gut microbial profiles in premature infants fed with breast milk and donor human milk, however, it is not known how this affects the species composition of the genus Bifidobacterium. The objective of this study was to assess the effect of donated human milk on shaping the gut bifidobacterial populations of premature babies during the first three months of life. We analyzed the gut bifidobacterial communities of 42 premature babies fed with human donor milk or own-mother milk by the 16S rRNA-23S rRNA internal transcriber spaces (ITS) region sequencing and q-PCR. Moreover, metabolic activity was assessed by gas chromatography. We observed a specific bifidobacterial profile based on feeding type, with higher bifidobacterial diversity in the human donor milk group. Differences in specific Bifidobacterium species composition may contribute to the development of specific new strategies or treatments aimed at mimicking the impact of own-mother milk feeding in neonatal units

RF plasma cleaning of optical surfaces: A study of cleaning rates on different carbon allotropes as a function of RF powers and distances

An extended study on an advanced method for the cleaning of carbon contaminations on large optical surfaces using a remote inductively coupled low pressure RF plasma source (GV10x downstream asher) is reported in this work. Technical as well as scientific features of this scaled up cleaning process are analyzed, such as the cleaning efficiency for different carbon allotropes (amorphous and diamond-like carbon) as a function of feedstock gas composition, RF power (ranging from 30 to 300W), and source-object distances (415 to 840 mm). The underlying physical phenomena for these functional dependences are discussed.Comment: 16 pages, 9 figure

Effect of intrapartum antibiotics prophylaxis on the bifidobacterial establishment within the neonatal gut

Antibiotics are important disruptors of the intestinal microbiota establishment, linked to immune and metabolic alterations. The intrapartum antibiotics prophylaxis (IAP) is a common clinical practice that is present in more than 30% of labours, and is known to negatively affect the gut microbiota composition. However, little is known about how it affects to Bifidobacterium (sub)species level, which is one of the most important intestinal microbial genera early in life. This study presents qualitative and quantitative analyses of the bifidobacterial (sub)species populations in faecal sam-ples, collected at 2, 10, 30 and 90 days of life, from 43 healthy full-term babies, sixteen of them delivered after IAP use. This study uses both 16S rRNA–23S rRNA internal transcribed spacer (ITS) region sequencing and q-PCR techniques for the analyses of the relative proportions and absolute levels, respectively, of the bifidobacterial populations. Our results show that the bifidobacterial populations establishment is affected by the IAP at both quantitative and qualitative levels. This practice can promote higher bifidobacterial diversity and several changes at a compositional level. This study underlines specific targets for developing gut microbiota-based products for favouring a proper bifidobacterial microbiota development when IAP is required