Optimal illumination scheme for isotropic quantitative differential phase contrast microscopy

Differential phase contrast microscopy (DPC) provides high-resolution quantitative phase distribution of thin transparent samples under multi-axis asymmetric illuminations. Typically, illumination in DPC microscopic systems is designed with 2-axis half-circle amplitude patterns, which, however, result in a non-isotropic phase contrast transfer function (PTF). Efforts have been made to achieve isotropic DPC by replacing the conventional half-circle illumination aperture with radially asymmetric patterns with 3-axis illumination or gradient amplitude patterns with 2-axis illumination. Nevertheless, these illumination apertures were empirically designed based on empirical criteria related to the shape of the PTF, leaving the underlying theoretical mechanisms unexplored. Furthermore, the frequency responses of the PTFs under these engineered illuminations have not been fully optimized, leading to suboptimal phase contrast and signal-to-noise ratio (SNR) for phase reconstruction. In this Letter, we provide a rigorous theoretical analysis about the necessary and sufficient conditions for DPC to achieve perfectly isotropic PTF. In addition, we derive the optimal illumination scheme to maximize the frequency response for both low and high frequencies (from 0 to 2N Aob j), and meanwhile achieve perfectly isotropic PTF with only 2-axis intensity measurements. We present the derivation, implementation, simulation and experimental results demonstrating the superiority of our method over state-of-the-arts in both phase reconstruction accuracy and noise-robustness.https://arxiv.org/abs/1903.10718Accepted manuscrip

Extinction Pattern of Reef Ecosystems in Latest Permian

Studies of two Permian-Triassic boundary (PTB) sections on top of a Changhsingian reef in Ziyun, Guizhou Province, southwestern China indicate that the end-Permian mass extinction of reef ecosystems occurred in two steps. The first step is the extinction of all stenotropic organisms such as calcisponges and fusulinids in the latest Permian (in the Clarkina yini conodont zone). The biota after the first extinction is simple, comprising eurytropic organisms including microgastropods, ostracods, and some small burrowing organisms, or only algal mats. At the beginning of the Early Triassic (i.e. the beginning of the Hindeodus parvus zone), the environments became anoxic, and the microgastropod dominated biota or algal mats disappeared, which constituted the second episode of the mass extinction. The biota after the second extinction comprises small spherical microproblematica, some kinds of specialized organisms tolerant of anoxic or oxygen-poor conditions. As the environments became oxygenated, the specialized biota was replaced by a microgastropod-dominated simple biota. When the environmental conditions improved further, the simple biota was replaced by a diverse biota with normal-sized ammonoids, bivalves, and gastropods, representing restoration of normal oceanic conditions. Comparison with PTB sections in Dolomites, Italy and Meishan, Zhejiang Province shows that non-reef ecosystems had a similar first episode of mass extinction in the latest Permian. In the case that oceanic anoxia happened, non-reef ecosystems had a second extinction episode similar to that of reef ecosystems

Optimal illumination scheme for isotropic quantitative differential phase contrast microscopy

Differential phase contrast microscopy (DPC) provides high-resolution quantitative phase distribution of thin transparent samples under multi-axis asymmetric illuminations. Typically, illumination in DPC microscopic systems is designed with 2-axis half-circle amplitude patterns, which, however, result in a non-isotropic phase contrast transfer function (PTF). Efforts have been made to achieve isotropic DPC by replacing the conventional half-circle illumination aperture with radially asymmetric patterns with 3-axis illumination or gradient amplitude patterns with 2-axis illumination. Nevertheless, these illumination apertures were empirically designed based on empirical criteria related to the shape of the PTF, leaving the underlying theoretical mechanisms unexplored. Furthermore, the frequency responses of the PTFs under these engineered illuminations have not been fully optimized, leading to suboptimal phase contrast and signal-to-noise ratio (SNR) for phase reconstruction. In this Letter, we provide a rigorous theoretical analysis about the necessary and sufficient conditions for DPC to achieve perfectly isotropic PTF. In addition, we derive the optimal illumination scheme to maximize the frequency response for both low and high frequencies (from 0 to 2NAobj), and meanwhile achieve perfectly isotropic PTF with only 2-axis intensity measurements. We present the derivation, implementation, simulation and experimental results demonstrating the superiority of our method over state-of-the-arts in both phase reconstruction accuracy and noise-robustness.Comment: 18 pages, 9 figure

Quantitative Phase Imaging Camera With a Weak Diffuser

We introduce the quantitative phase imaging camera with a weak diffuser (QPICWD) as an effective scheme of quantitative phase imaging (QPI) based on normal microscope platforms. The QPICWD is an independent compact camera measuring object induced phase delay under low-coherence quasi-monochromatic illumination by examining the deformation of the speckle intensity pattern. By interpreting the speckle deformation with an ensemble average of the geometric flow, we can obtain the high-resolution distortion field via the transport of intensity equation (TIE). Since the phase measured by TIE is the generalized phase of the partially coherent image, rather than the phase of the measured object, we analyze the effect of illumination coherence and imaging numerical aperture (NA) on the accuracy of phase retrieval, revealing that the sample's phase can be reliably reconstructed under the conditions that the coherence parameter (the ratio of illumination NA to objective NA) of the Köhler illumination is between 0.3 and 0.5. We present some applications for the proposed design involving nondestructive optical testing of microlens array with nanometric thickness and imaging of fixed and live unstained HeLa cells. Since the designed QPI camera does not require any modification of the widely available bright-field microscope or additional accessories for its use, it is expected to be applied by the broader communities of biology and medicine

Effects of exogenous retinoic acid on ocular parameters in Guinea pigs with form deprivation myopia

Aim: Myopia is a common chronic eye disease, this study is to investigate the effects of exogenous retinoic acid (RA) on intraocular parameters, especially choroidal thickness (CT) and retinal thickness (RT), in guinea pigs with form deprivation myopia (FDM).Methods: A total of 80 male guinea pigs were divided randomly into 4 groups: Control, FDM, FDM + RA, and FDM + Citral groups. The FDM + RA group was given 24 mg/kg RA dissolved in 0.4 mL peanut oil; the FDM + Citral group was given citral 445 mg/kg dissolved in 0.4 mL peanut oil; The other two groups were given 0.4 mL peanut oil. After 4 weeks, the refractive error (RE), axial length (AL), and intraocular pressure (IOP) of all guinea pigs were measured, and the parameters of RT and CT were obtained using enhanced depth imaging optical coherence tomography (EDI-OCT).Results: After 4 weeks, both the RE and AL in the FDM and FDM + RA groups were increased, and the RT and CT in both groups were smaller than those in the Control group (p < 0.05). Only the IOP of the right eye in the FDM + RA group increased significantly (p < 0.05). The RT of the right eye of the 4 groups was compared: Control group > FDM + Citral group > FDM group > FDM + RA group. Compared with the RT of the left eye and the right eye among the 4 groups, the RT of the right eye in the FDM and FDM + RA groups was significantly less than that in the left eye (p < 0.05). Moreover, the CT of the right eye in the Control group was greater than that in the other three groups (p < 0.0001). There was no significant difference in the CT among the FDM, FDM + RA, and FDM + Citral groups (p > 0.05). In contrast to the RT results, the CT results of the left and right eyes in the FDM + Citral group showed statistically significant differences (p < 0.05).Conclusion: RA participates in the progression of FDM as a regulatory factor. Exogenous RA can increase the RE, AL, and IOP of FDM guinea pigs, and might aggravate the retinal thinning of FDM guinea pigs. Citral can inhibit these changes, but RA might not affect the thickness of the choroid

Ascorbic Acid Facilitates Neural Regeneration After Sciatic Nerve Crush Injury

Ascorbic acid (AA) is an essential micronutrient that has been safely used in the clinic for many years. The present study indicates that AA has an unexpected function in facilitating nerve regeneration. Using a mouse model of sciatic nerve crush injury, we found that AA can significantly accelerate axonal regrowth in the early stage [3 days post-injury (dpi)], a finding that was revealed by immunostaining and Western blotting for antibodies against GAP-43 and SCG10. On day 28 post-injury, histomorphometric assessments demonstrated that AA treatment increased the density, size, and remyelination of regenerated axons in the injured nerve and alleviated myoatrophy in the gastrocnemius. Moreover, the results from various behavioral tests and electrophysiological assays revealed that nerve injury-derived functional defects in motor and sensory behavior as well as in nerve conduction were significantly attenuated by treatment with AA. The potential mechanisms of AA in nerve regeneration were further explored by investigating the effects of AA on three types of cells involved in this process [neurons, Schwann cells (SCs) and macrophages] through a series of experiments. Overall, the data illustrated that AA treatment in cultured dorsal root ganglionic neurons resulted in increased neurite growth and lower expression of RhoA, which is an important inhibitory factor in neural regeneration. In SCs, proliferation, phagocytosis, and neurotrophin expression were all enhanced by AA. Meanwhile, AA treatment also improved proliferation, migration, phagocytosis, and anti-inflammatory polarization in macrophages. In conclusion, this study demonstrated that treatment with AA can promote the morphological and functional recovery of injured peripheral nerves and that this effect is potentially due to AA’s bioeffects on neurons, SCs and macrophages, three of most important types of cells involved in nerve injury and regeneration

Petrologic Evidence for Sea-Level Drop in Latest Permian in Jiangxi Province, China and its Meanings for the Mass Extinction

A new-found Permian-Triassic boundary section in Xiushui, Jiangxi Province, China shows evidence for sea-level drop during the latest Permian. Evidence for sea-level drop was preserved in a 2.1 m thick interval of limestone, and is 1 m from the P-T boundary. The basal 0.1 m of this interval is a reddish sparry-cemented grainstone. The grains are rounded, dolomitized, all having a black coating. Microprobe analysis indicates that the coating is limonite, which indicates a weathering event in subaerial environments after a sea-level drop event. The internal structure of most grains has been destroyed by diagenesis. Some remained structures of foraminifers and fusulinids. So, this bed is formed before the mass extinction. The 2.0 m thick bed overlying the reddish grainstone is a dedolomitized limestone. The shapes of some original finely-crystalline dolomite rhombus were preserved. The occurrence of dedolomitization is generally related to meteoric water. So, this bed recorded a sea-level drop event. Fossils in this bed are simple: fusulinids and large foraminifers such as Colaniella are absent. It is clear that mass extinction began before this bed. The 1 m thick limestone between the dedolomitized bed and the P-T boundary is composed of grainstone and lime mudstone. Study of this section reached two points: (1) sea-level drop occurred in latest Permian; (2) The end-Permian mass extinction began in the earliest episode of the sea-level drop event. Thus, we cannot exclude the possibility that the mass extinction was caused by a dramatic environmental change which triggered the end-Permian sea-level drop

Microbialite of Anoxic Condition from Permian-Triassic Transition in Guizhou, China

Spherical microfossils are present in the Hindeodus parvus zone of the Lower Triassic in Ziyun, Guizhou Province. They generally range from 0.15 to 0.30 mm across, with micritic wall and filled by micro-sparry calcites, and are evenly scattered in micritic matrix. Their abundance makes the rock assigned to microbialites. The accompanied organisms include ostracods and algal mat, but no gastropods or bivalves. Presence of small (\u3c7 μm) pyrite framboids indicates that this bed formed in anoxic conditions. In some sections, this bed is overlain and underlain by tidal-flat micritic limestone with microgastropods and small burrows. Occurrence only in deposits on reef top indicates that the microbial organism was benthic, and needed sunlight in life. The size of the microbial fossil exceeds that of any bacteria or cyanobacteria. Thus, it does not belong to these two phyla. It may belong to lower green algae, and is assigned to a new species in a new genus, Ziyunosphaeridium sinensis gen. et sp. nov. Up to now, the rocks described as microbialites from the Permian-Triassic transition include six types: (1) porous micritic limestone such as that descried from Japan by Sano and Nakashima (1997), (2) limestone with rich globular microfossils such as that described from the Nanpanjiang Basin in China by Lehrmann (1999), (3) dendroidal limestone such as that described from the vicinity of Chongqing by Kershaw et al. (1999), (4) spherical microbial limestone adapted to anoxic environments described from Ziyun, Guizhou reported in this paper, (5) limestone with cyanobacterial fossils such as that described by Wang et al. (2005), and (6) stromatolites. All these microbialites are not reefs in the proper sense, and the argument that Permian reef ecosystems extended into the Mesozoic is incorrect

A New Fast Algorithm for Constrained Four-Directional Total Variation Image Denoising Problem

International audienceA new four-directional total variation (4-TV) model, applicable to isotropic and anisotropic TV functions, is proposed for image denoising. A dual based fast gradient projection algorithm for the constrained 4-TV image denoising problem is also reported which combines the well-known gradient projection and the fast gradient projection methods. Experimental results show that this model provides in most cases a better signal to noise ratio when compared to previous models like the reference TV, the total generalized variation, and the nonlocal total variatio