RotatedStomataNet: a deep rotated object detection network for directional stomata phenotype analysis

KEY MESSAGE

Innovatively, we consider stomatal detection as rotated object detection and provide an end-to-end, batch, rotated, real-time stomatal density and aperture size intelligent detection and identification system, RotatedeStomataNet. Stomata acts as a pathway for air and water vapor in the course of respiration, transpiration, and other gas metabolism, so the stomata phenotype is important for plant growth and development. Intelligent detection of high-throughput stoma is a key issue. Nevertheless, currently available methods usually suffer from detection errors or cumbersome operations when facing densely and unevenly arranged stomata. The proposed RotatedStomataNet innovatively regards stomata detection as rotated object detection, enabling an end-to-end, real-time, and intelligent phenotype analysis of stomata and apertures. The system is constructed based on the Arabidopsis and maize stomatal data sets acquired destructively, and the maize stomatal data set acquired in a non-destructive way, enabling the one-stop automatic collection of phenotypic, such as the location, density, length, and width of stomata and apertures without step-by-step operations. The accuracy of this system to acquire stomata and apertures has been well demonstrated in monocotyledon and dicotyledon, such as Arabidopsis, soybean, wheat, and maize. The experimental results that the prediction results of the method are consistent with those of manual labeling. The test sets, the system code, and their usage are also given ( https://github.com/AITAhenu/RotatedStomataNet ).

The conundrum of olecranon aperture and its relation to the distal end of the humerus in a modern Indian population: An anatomical and surgical perspective

PURPOSE

We aimed to clarify the morphology of the olecranon aperture (OA) of the humerus with its relationship to the distal end of the humerus (epicondylar width) and the width of the medullary canal.

METHODS

In total, 156 dry adult humeri were examined for the presence of OA. When present, we reported their shape, measured transverse (TD) and vertical diameter (VD), the distance from its medial border to the tip of medial epicondyle (D1), lateral border to the tip of lateral epicondyle (D2) and lower border to the tip of trochlea (D3). The epicondylar width (EW) and the width of the medullary canal were also measured in all the humeri.

RESULTS

OA was reported in 32 humeri (20.6%) with left side predominance, translucent septum in 35.8%, and opaque septum in 43.6%. The most typical shape noted was oval. On right side, mean VD and TD was 4.30±0.54mm and 5.85±0.45mm, respectively, whereas on left, these value were 4.21±0.56mm and 5.64±0.43mm, respectively. The mean of D1, D2 and D3 was 25.86±0.43mm, 26.50±0.28mm and 15.07±0.53mm on right and 24.80±0.41mm, 26.84±0.21mm and 15.81±0.31mm on left with significant difference (P<0.05). The medullary canal was significantly smaller in humeri with OA.

CONCLUSION

Topographic location of OA may have possible role in determining safe zone for retrograde nailing in supracondylar humeral fractures. Since OA has a direct relation to the size of the intramedullary canal, it is crucial during preoperative planning and choosing an adequate surgical approach involving lower segment of humerus.

Implementation of apertures in a proton pencil-beam dose algorithm

The use of field-specific apertures, routine in scattered or uniform-scanned proton fields, are still a necessity in pencil-beam scanned (PBS) fields to sharpen the penumbral edge at low energies and in high fraction dose application beyond that achievable with small spot size. We describe a model implemented in our clinical pencil-beam algorithm that models the insertion of a shaped aperture, including shapes adapted per energy layer such as may be achieved with a multi-leaf collimator. The model decomposes the spot transport into discrete steps. The first step transport a uniform intensity field of high-resolution sub-pencil-beams at the layer energy through the medium. This transport only considers primary scattering in both the patient and an optional range-shifter. The second step models the aperture areas and edge penumbral transition as a modulation of the uniform intensity. The third step convolves individual steps over the uniform-transported field including the aperture-modified intensities. We also introduce an efficient model based on a Clarkson sector integration for nuclear scattered halo protons. This avoids the explicit modeling of long range halo protons to the detriment of computational efficiency in calculation and optimization. We demonstrate that the aperture effect is primarily due to in-patient and shifter scattering with a small contribution from the apparent beam source position. The model provides insight into the primary physics contributions to the penumbra and the nuclear halo. The model allowed us to fully deploy our PBS capacity at our two-gantry center without which PBS treatments would have been inferior compared to scattered fields with apertures. Finally, Monte Carlo calculations have (nearly) replaced phenomenological pencil-beam models for collimated fields. Phenomenological models do, however, allow exposition of underlying clinical phenomena and closer connection to representative clinical observables.

Investigating the utilization of beam-specific apertures for the intensity-modulated proton therapy (IMPT) head and neck cancer plans

Intensity-modulated proton therapy (IMPT) planning for the head and neck (HN) cancer often requires the use of the range shifter, which can increase the lateral penumbrae of the pencil proton beam in the patient, thus leading to an increase in unnecessary dose to the organs at risks (OARs) in proximity to the target volumes. The primary goal of the current study was to investigate the dosimetric benefits of utilizing beam-specific apertures for the IMPT HN cancer plans. The current retrospective study included computed tomography datasets of 10 unilateral HN cancer patients. The clinical target volume (CTV) was divided into low-risk CTV1 and high-risk CTV2. Total dose prescriptions to the CTV1 and CTV2 were 54 Gy(RBE) and 70 Gy(RBE), respectively, with a fractional dose of 2 Gy(RBE). All treatment plans were robustly optimized (patient setup uncertainty = 3 mm; range uncertainty = 3.5%) on the CTVs. For each patient, 2 sets of plans were generated: (1) without beam-specific aperture (WOBSA), and (2) with beam-specific aperture (WBSA). Specifically, both the WOBSA and WBSA of the given patient used identical beam angles, air gap, optimization structures, optimization constraints, and optimization settings. Target coverage and homogeneity index were comparable in both the WOBSA and WBSA plans with no statistical significance (p > 0.05). On average, the mean dose in WBSA plans was reduced by 12.1%, 2.9%, 3.0%, 3.8%, and 5.2% for the larynx, oral cavity, parotids, superior pharyngeal constrictor muscle, and inferior pharyngeal constrictor muscle, respectively. The dosimetric results of the OARs were found to be statistically significant (p < 0.05). The use of the beam-specific apertures did not deteriorate the coverage and homogeneity in the target volume and allowed for a reduction in mean dose to the OARs with an average difference up to 12.1%.

Imaging of a retinal pigment epithelium aperture using polarization-sensitive optical coherence tomography

PURPOSE

To evaluate cases with a retinal pigment epithelium (RPE) aperture using polarization-sensitive optical coherence tomography (PS-OCT).

STUDY DESIGN

Retrospective consecutive case series.

METHODS

A retrospective study that included three eyes (three patients) with RPE aperture and age-related macular degeneration (AMD) evaluated at the Macular Clinic in Tokyo University Hospital. A three-dimensional dataset of depolarization information was obtained with a clinical prototype of PS-OCT.

RESULTS

All patients were categorized as intermediate AMD. RPE apertures were identified with PS-OCT as discontinuities of depolarization in the RPE layer of the pigment epithelial detachment (PED). A nonuniform decrease of depolarization in the RPE layer was also observed around the aperture. Two findings were observed above the aperture, intraretinal focal areas with high reflectivity and increased depolarization and subretinal bands with moderate reflectivity and low depolarization. Retinal sensitivity according to fundus microperimetry measured at 25 points was significantly associated with the degree of depolarization at the corresponding area (r-square = 0.60, p = 0.0001).

CONCLUSION

The RPE aperture was characterized as a round discontinuity of depolarization. The findings with PS-OCT suggest atrophic changes in the overlying RPE of the PED. The degree of depolarization was associated with retinal sensitivity. The current results indicate that RPE apertures developed within the spectrum of atrophic AMD.

Eyelid squinting during food pecking in pigeons

The visual control of pecking by pigeons (Columba livia) has latterly been thought to be restricted to the fixation stops interrupting their downward head movements because these stops prevent interference by motion blur. Pigeons were also assumed to close their eyes during the final head thrust of the peck. Here, we re-examined their pecking motions using high-speed video recordings and supplementary provisions that permitted a three-dimensional spatial analysis of the movement, including measurement of pupil diameter and eyelid slit width. The results confirm that pigeons do not close their eyes completely during the presumed optically ballistic phase of pecking. Instead, their eyelids are narrowed to a slit. The width of this slit is sensitive to both the ambient illumination level and the visual background against which seed targets have to be detected and grasped. There is also evidence of some interaction between pupil diameter and eyelid slit width. We surmise that besides being an eye-protecting reflex, the partial covering of the pupil with the eyelids may increase the depth of focus, enabling pigeons to obtain sharp retinal images of peck target items at very close range and during the beak-gape 'handling' of food items and occasional grit particles.

Obtaining diffraction patterns from annular dark-field STEM-in-SEM images: Towards a better understanding of image contrast

This contribution demonstrates experimentally how a series of annular dark-field transmission images collected in a scanning electron microscope (SEM) with a basic solid-state detector can be used to quantify electron scattering distributions (i.e., diffraction patterns). The technique is demonstrated at different primary electron energies with a polycrystalline aluminum sample and two amorphous samples comprising vastly different mass-thicknesses. Contrast reversal is demonstrated in both amorphous samples, suggesting that intuitive image contrast interpretation is not always straightforward even for ultrathin, low atomic number samples. We briefly address how the scattering distributions obtained here can be used as an aid to interpret contrast in annular dark-field images, and how to set up imaging conditions to obtain intuitively interpretable contrast from samples with regions of significantly different thickness.

Congenital nasal pyriform aperture stenosis: Analysis of twenty cases at a single institution

OBJECTIVES

Congenital nasal pyriform aperture stenosis (CNPAS) is a rare cause of neonatal respiratory distress that is difficult to treat. The primary objective of this study was to identify factors that predict the need for initial and revision surgery for CNAPS. The secondary objective is to identify risk factors in maternal history associated with the development of CNPAS.

METHODS

Infants with CNPAS between 2010 and 2017 were identified by ICD- 9 and 10 codes. Demographics, maternal history, anatomic features on imaging and medical and/or surgical management were reviewed. Frequencies, means and standard deviations were calculated. A p-value <.05 was considered significant.

RESULTS

Twenty infants were included. All underwent flexible nasal endoscopy with inability to pass the scope in either nostril in 65% of infants. Nineteen had a CT scan and 13 had a MRI with midline defects in 76.3% and 53.8%, respectively. Solitary central mega-incisor was present in 65%. Half underwent surgical intervention at a mean age of 74.8 days, with 90% requiring revision surgery. There was no difference in pyriform aperture distance in the surgical and non-surgical patient subgroups (5.4 mm and 5.2 mm, p = .6 respectively). No specific variables were predictive of need for initial or revision surgery. Maternal diabetes mellitus (MDM) was found in 55% of mothers of infants with CNPAS.

CONCLUSION

Pyriform aperture distance was not a predictor of surgical intervention. MRI should be considered in all infants with CNPAS as the rate of intracranial complications is high. MDM may be a risk factor for CNPAS.

Virtual auditory aperture passability

Two experiments investigated (1) the ability of individuals to perceive the passability of apertures that are constructed using two virtual sounds sources and (2) the nature of the perceptual information that is used when determining passability in such a way. In the first experiment, participants judged whether they could successfully walk between two sound sources, heard through headphones, without turning their shoulders. We hypothesized that judgements would be accurate and driven by the detection of a proposed informational variable that relates head rotation, forward locomotion and aperture width. To test this hypothesis, we used motion tracking and a gain manipulation to alter apparent head rotation relative to virtual sound source positions and evaluated the effect on performance. Participants were able to accurately judge aperture passability based only on acoustic information. However, the gain manipulation did not show a significant influence on perceptual reports. The unexpected significant influence of lateral head movement on perceptual accuracy, however, does suggest that an alternative informational variable, based on lateral movement, may have been used. In the second experiment, a group of participants with wide shoulders was compared to a group with narrow shoulders on a similar task. Significant differences in minimally acceptable aperture width were found between the wide and narrow groups. When these aperture widths were scaled to the participants' shoulder widths, however, the differences were no longer present. These findings are consistent with previous studies investigating perception of passability and offer promising applications of virtual reality technology in the study of auditory perceptual abilities.

Characterization of the tissue crossing the supratrochlear aperture of the humerus using histochemical techniques

INTRODUCTION

The supratrochlear aperture (STA) is the opening observed in the septum that separates the olecranon from the coronoid fossae. Numerous studies have shown that there is considerable variation in the occurrence of this feature within and among populations.

MATERIALS AND METHODS

Cadavers (n = 43) were assessed for the presence of the STA by means of X-ray. Ten samples of STA-bearing bones and an equal number of controls without STA were obtained from cadavers using a hole saw. These samples were decalcified, fixed in formalin and processed for histological assessment in differing (ascending) grades of alcohol before being embedded in paraffin wax. Sections (10 µm thick) were stained with haematoxylin and eosin (H&E) for general architecture as well as the rapid one-step Mallory-Heidenhain stain for bone and connective tissue.

RESULTS

The STA samples exhibited an abundance of connective tissue arranged in regular bundles of fibers across the STA. In contrast, the controls showed only bone tissue in the septum.

DISCUSSION AND CONCLUSION

The arrangement of connective tissue fibers organized in regular bundles is a characteristic of strength, which may indicate that the STA is under sustained stress or pressure from the olecranon and coronoid processes of the ulna. It remains debatable whether the STA should continue to be considered as a foramen in life as we demonstrate that it is obliterated by connective tissue. It contains no neurovascular structures, making it unlike other structures defined as foramina.

Formation of pollen apertures in Arabidopsis requires an interplay between male meiosis, development of INP1-decorated plasma membrane domains, and the callose wall

In most plant species, surfaces of pollen grains display characteristic patterns of apertures, formed by the gaps in the pollen wall exine. The aperture patterns are species-specific and tend to be very precise, with pollen of each species usually developing a certain number of apertures placed at distinct positions and acquiring specific morphology. The precision with which pollen apertures are produced suggests that developing pollen grains possess robust mechanisms that allow them to specify particular membrane domains as the future-aperture sites and to protect these sites from exine deposition. Recently, we demonstrated that formation of apertures in Arabidopsis depends on certain membrane domains attracting a novel protein, INP1, that assembles into punctate lines and helps to anchor these membrane domains to the overlying callose wall. Here we show that in the absence of male meiosis the ability of INP1 to assemble into lines at the pollen surface is compromised. However, INP1 still arrives to the pollen surface and mediates the interactions between the plasma membrane and the callose wall, potentially contributing to the formation of grossly abnormal patterns on pollen surface.

A new method for estimating the extinction efficiency of polystyrene microsphere by micro-FTIR spectroscopy

The IR spectra of a single, isolated polystyrene sphere with diameter of 4.46μm under different aperture sizes have been measured by Micro-FTIR spectrometer and the scattering signal can be seen obviously. Based on Mie scattering theory, a feasible method has been proposed to estimate the extinction efficiency (Q_ext) of microsphere. Q_ext from Mid-IR spectroscopy is consistent well with that derived from MiePlot software. It shows that the extinction efficiency of microsphere with the size of the Mid-IR range (2.5μm-25μm), which exhibits weak IR absorption, can be obtained by using the present method based on recorded Micro-FTIR spectra.

Aperture extent and stimulus speed affect the perception of visual acceleration

Humans are generally poor at detecting the presence of visual acceleration, but it is unclear whether the extent of a field of moving objects through an aperture affects this ability. Hypothetically, the farther a stimulus can accelerate uninterrupted by an aperture's physical constraints, the easier it should be to discern its motion profile. We varied the horizontal extent of the aperture through which continuously accelerating or decelerating random dot arrays were presented at different average speeds, and measured acceleration and deceleration detection thresholds. We also hypothesized that manipulating aperture extent at different speeds would change how observers visually pursue acceleration, which we tested in a control experiment. Results showed that, while there was no difference between the acceleration and deceleration conditions, detection was better in the larger than small aperture conditions. Regardless of aperture size, smaller acceleration and deceleration rates (relative to average speed) were needed to detect changing speed in faster than slower speed ranges. Similarly, observers tracked the stimuli to a greater extent in the larger than small apertures, and smooth pursuit was overall poorer at faster than slower speeds. Notably, the effect of speed on pursuit was greater for the larger than small aperture conditions, suggesting that the small aperture restricted pursuit. Furthermore, there was little difference in psychophysical and eye movement data between the medium and large aperture conditions within each speed range, indicating that it is easier to detect an accelerating profile when the aperture is large enough to encourage a minimum level of pursuit.

Porosity, permeability and 3D fracture network characterisation of dolomite reservoir rock samples

With fractured rocks making up an important part of hydrocarbon reservoirs worldwide, detailed analysis of fractures and fracture networks is essential. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) however suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this paper, we therefore explore the use of an additional method - non-destructive 3D X-ray micro-Computed Tomography (μCT) - to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. We process the 3D μCT data in this study by a Hessian-based fracture filtering routine and can successfully extract porosity, fracture aperture, fracture density and fracture orientations - in bulk as well as locally. Additionally, thin sections made from selected plug samples provide 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) towards more realistic reservoir conditions. This study shows that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that although there are limitations, several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other methods can therefore be a powerful approach in microstructural analysis of reservoir rocks, especially when applying the concepts that we present (on a small set of samples) in a larger study, in an automated and standardised manner.

The fundus slit lamp

Fundus biomicroscopy with the slit lamp as it is practiced widely nowadays was not established until the 1980-es with the introduction of the Volk lenses +90 and +60D. Thereafter little progress has been made in retinal imaging with the slit lamp. It is the aim of this paper to fully exploit the potential of a video slit lamp for fundus documentation by using easily accessible additions.

Suitable still images are easily retrieved from videorecordings of slit lamp examinations. The effects of changements in the slit lamp itself (slit beam and apertures) and its examination equipment (converging lenses from +40 to +90D) on quality and spectrum of fundus images are demonstrated. Imaging software is applied for reconstruction of larger fundus areas in a mosaic pattern (Hugin®) and to perform the flicker test in order to visualize changes in the same fundus area at different points of time (Power Point®).

The three lenses +90/+60/+40D are a good choice for imaging the whole spectrum of retinal diseases. Displacement of the oblique slit light can be used to assess changes in the surface profile of the inner retina which occurs e.g. in macular holes or pigment epithelial detachment. The mosaic function in its easiest form (one strip macula adapted to one strip with the optic disc) provides an overview of the posterior pole comparable to a fundus camera’s image. A reconstruction of larger fundus areas is feasible for imaging in vitreoretinal surgery or occlusive vessel disease. The flicker test is a fine tool for monitoring progressive glaucoma by changes in the optic disc, and it is also a valuable diagnostic tool in macular disease.

Nearly all retinal diseases can be imaged with the slit lamp - irrespective whether they affect the posterior pole, mainly the optic nerve or the macula, the whole retina or only its periphery. Even a basic fundus controlled perimetry is possible. Therefore fundus videography with the slit lamp is a worthwhile approach especially for the many ophthalmologists without access to the most recent diagnostic equipment or a professional photographer at hand.

Imaging ultrasonic dispersive guided wave energy in long bones using linear radon transform

Multichannel analysis of dispersive ultrasonic energy requires a reliable mapping of the data from the time-distance (t-x) domain to the frequency-wavenumber (f-k) or frequency-phase velocity (f-c) domain. The mapping is usually performed with the classic 2-D Fourier transform (FT) with a subsequent substitution and interpolation via c = 2πf/k. The extracted dispersion trajectories of the guided modes lack the resolution in the transformed plane to discriminate wave modes. The resolving power associated with the FT is closely linked to the aperture of the recorded data. Here, we present a linear Radon transform (RT) to image the dispersive energies of the recorded ultrasound wave fields. The RT is posed as an inverse problem, which allows implementation of the regularization strategy to enhance the focusing power. We choose a Cauchy regularization for the high-resolution RT. Three forms of Radon transform: adjoint, damped least-squares, and high-resolution are described, and are compared with respect to robustness using simulated and cervine bone data. The RT also depends on the data aperture, but not as severely as does the FT. With the RT, the resolution of the dispersion panel could be improved up to around 300% over that of the FT. Among the Radon solutions, the high-resolution RT delineated the guided wave energy with much better imaging resolution (at least 110%) than the other two forms. The Radon operator can also accommodate unevenly spaced records. The results of the study suggest that the high-resolution RT is a valuable imaging tool to extract dispersive guided wave energies under limited aperture.

Generalization of the Matsumoto-Tonomura approximation for the phase shift within an open aperture

As shown by Matsumoto and Tonomura, the phase shift imposed on an electron beam by an electrostatic phase plate is constant for all (straight) electron trajectories passing through a circular aperture, provided that (1) the electric field goes to zero at distances far above and below the aperture and (2) the value of the phase shift at the boundary (i.e. perimeter of the aperture) is constant [5]. We now point out that the result can be valid for any shape of the hole in the aperture, and, furthermore, it requires only that the electric field is equal and opposite at large distances above and below the aperture, respectively. We also point out that the conditions of validity of the Matsumoto-Tonomura approximation constrain the phase shift across the open aperture to a quadratic algebraic form when the phase shift is not constant around the perimeter. Finally, it follows that the projection approximation for calculating the phase shift must fail for strong phase shifts of higher than quadratic form. These extensions of the original result of Matsumoto and Tonomura give further insight to the analysis of charging phenomena observed with apertures that are designed to produce contrast in in-focus images of weak phase objects.