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

Morphological indicators of growth response of coniferous advance regeneration to overstorey removal in the boreal forest

Regeneration of forest stands through the preservation of existing advance regeneration has gained considerable interest in various regions of North America. The effectiveness of this approach relies on the capacity of regeneration to respond positively to overstory removal. Responses of advance regeneration to release is dependent on tree characteristics and site conditions interacting with the degree of physiological shock caused by the sudden change in environmental conditions. This paper presents a review of the literature describing the relationships between morphological indicators and the advance regeneration response to canopy removal. It focuses primarily on the following species: jack pine (Pinus banksiana Lamb.), lodgepole pine (Pinus contorta Dougl. var. latifolia Engelm.), black spruce (Picea mariana (Mill.) B.S.P.), interior spruce (Picea glauca x engelmannii), white spruce (Picea glauca (Moench) Voss), balsam fir (Abies balsamea (L.) Mill.), and subalpine fir (Abies lasiocarpa (Hook.) Nutt). Pre-release height growth has been found to be a good indicator of post-release response for many species. Live-crown ratio also appears to be a good indicator of vigour for shade-tolerant species. The ratio of leader length to length of the longest lateral at the last whorl could serve to describe the degree of suppression before harvest for shade-tolerant species. Number of nodal and internodal branches or buds has been found to be related with vigour for many species. Logging damage has been shown to be an important determinant of seedling response to overstory removal. In contrast, height/diameter ratio has limited value for predicting response to release since it varies with site, species and other factors. No clear relationship between age, height at release and response to release could be demonstrated. This paper also suggests the use of combined indicators and critical threshold values for these indicators

Histological and cytological imaging using Fourier ptychographic microscopy

Structural imaging using light microscopy is a cornerstone of histology and cytology. However, the utility of the optical microscope for diagnostic imaging is limited by the fundamental tradeoff between the field of view and spatial resolution and a reliance on exogenous dyes to generate sufficient image contrast. Fourier Ptychographic Microscopy (FPM) is a complex imaging modality with the potential to overcome these limitations by recovering high-resolution images of sample amplitude and phase from a set of low-resolution raw images captured under inclined illumination. In this article we explore the application of FPM to clinical imaging using a simple, low-cost FPM system and simulated and experimental data to explore the influence of both image acquisition parameters and hardware configuration on image quality and imaging throughput. The practical performance of the method is investigated by imaging peripheral blood films and histological tissue sections. We find that, at the cost of increased computational complexity, FPM increases the information capture capacity of the optical microscope significantly, allowing label-free examination and quantification of features such as tissue and cell morphology over large sample areas

Functional ecology of advance regeneration in relation to light in boreal forests

This paper reviews aspects of the functional ecology of naturally established tree seedlings in the boreal forests of North America with an emphasis on the relationship between light availability and the growth and survival of shade tolerant conifers up to pole size. Shade tolerant conifer species such as firs and spruces tend to have a lower specific leaf mass, photosynthetic rate at saturation, live crown ratio, STAR (shoot silhouette area to total needle surface area ratio), and root to shoot ratio than the shade intolerant pines. The inability of intolerant species such as the pines and aspen to survive in shade appears to be mainly the result of characteristics at the shoot, crown, and whole-tree levels and not at the leaf level. Although firs and spruces frequently coexist in shaded understories, they do not have identical growth patterns and crown architectures. We propose a simple framework based on the maximum height that different tree species can sustain in shade, which may help managers determine the timing of partial or complete harvests. Consideration of these functional aspects of regeneration is important to the understanding of boreal forest dynamics and can be useful to forest managers seeking to develop or assess novel silvicultural systems

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

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

Depth-resolved local reflectance spectra measurements in full-field optical coherence tomography

Full-field optical coherence tomography (FF-OCT) is a widely used technique for applications such as biological imaging, optical metrology, and materials characterization, providing structural and spectral information. By spectral analysis of the backscattered light, the technique of spectroscopic-OCT enables the differentiation of structures having different spectral properties, but not the determination of their reflectance spectrum. For surface measurements, this can be achieved by applying a Fourier transform to the interferometric signals and using an accurate calibration of the optical system. An extension of this method is reported for local spectroscopic characterization of transparent samples and in particular for the determination of depth-resolved reflectance spectra of buried interfaces. The correct functioning of the method is demonstrated by comparing the results with those obtained using a program based on electromagnetic matrix methods for stratified media. Experimental measurements of spatial resolutions are provided to demonstrate the smallest structures that can be characterized

Smartphone screens as astrometric calibrators

Geometric optical distortion is a significant contributor to the astrometric error budget in large telescopes using adaptive optics. To increase astrometric precision, optical distortion calibration is necessary. We investigate using smartphone OLED screens as astrometric calibrators. Smartphones are low cost, have stable illumination, and can be quickly reconfigured to probe different spatial frequencies of an optical system's geometric distortion. In this work, we characterize the astrometric accuracy of a Samsung S20 smartphone, with a view towards providing large format, flexible astrometric calibrators for the next generation of astronomical instruments. We find the placement error of the pixels to be 189 nm +/- 15 nm RMS. At this level of error, milliarcsecond astrometric accuracy can be obtained on modern astronomical instruments.Comment: 15 pages, 11 figures; accepted, Journal of Astronomical Instrumentatio

Automatic inference of indexing rules for MEDLINE

This paper describes the use and customization of Inductive Logic Programming (ILP) to infer indexing rules from MEDLINE citations. Preliminary results suggest this method may enhance the subheading attachment module of the Medical Text Indexer, a system for assisting MEDLINE indexers.

Depth-resolved local reflectance spectra measurements in full-field optical coherence tomography

Full-field optical coherence tomography (FF-OCT) is a widely used technique for applications such as biological imaging, optical metrology, and materials characterization, providing structural and spectral information. By spectral analysis of the backscattered light, the technique of spectroscopic-OCT enables the differentiation of structures having different spectral properties, but not the determination of their reflectance spectrum. For surface measurements, this can be achieved by applying a Fourier transform to the interferometric signals and using an accurate calibration of the optical system. An extension of this method is reported for local spectroscopic characterization of transparent samples and in particular for the determination of depth-resolved reflectance spectra of buried interfaces. The correct functioning of the method is demonstrated by comparing the results with those obtained using a program based on electromagnetic matrix methods for stratified media. Experimental measurements of spatial resolutions are provided to demonstrate the smallest structures that can be characterized