A coded aperture microscope for X-ray fluorescence full-field imaging

The design and construction of an instrument for full-field imaging of the X-ray fluorescence emitted by a fully illuminated sample are presented. The aim is to produce an X-ray microscope with a few micrometers spatial resolution, which does not need to scan the sample. Since the fluorescence from a spatially inhomogeneous sample may contain many fluorescence lines, the optic which will provide the magnification of the emissions must be achromatic, i.e. its optical properties must be energy-independent. The only optics which fulfill this requirement in the X-ray regime are mirrors and pinholes. The throughput of a simple pinhole is very low, so the concept of coded apertures is an attractive extension which improves the throughput by having many pinholes, and retains the achromatic property. Modified uniformly redundant arrays (MURAs) with 10 µm openings and 50% open area have been fabricated using gold in a lithographic technique, fabricated on a 1 µm-thick silicon nitride membrane. The gold is 25 µm thick, offering good contrast up to 20 keV. The silicon nitride is transparent down into the soft X-ray region. MURAs with various orders, from 19 up to 73, as well as their respective negative (a mask where open and closed positions are inversed compared with the original mask), have been made. Having both signs of mask will reduce near-field artifacts and make it possible to correct for any lack of contrast.

Ex vivo full-field cellular-resolution optical coherence tomography of basal cell carcinomas: A pilot study of quality and feasibility of images and diagnostic accuracy in subtypes

BACKGROUND

Studies have reported the application of conventional optical coherence tomography (OCT) in the diagnosis of basal cell carcinoma (BCC). The new OCT provides cellular details similar to those in pathology slides and may reduce user learning time. This study aimed to demonstrate the quality of ex vivo full-field cellular-resolution OCT images and compare the diagnostic accuracy between physicians with varying pathology experience.

MATERIALS AND METHODS

Sixty histologically confirmed BCCs were selected. Tissue samples were sectioned and scanned using OCT, and their features were compared with those of hematoxylin and eosin (H&E)-stained sections. Thirty images were selected for the test administered to dermatology residents, dermatopathology fellows, and board-certified general pathologists without any OCT experience. The pretest learning included a 3-min instruction and 10-min self-study of four BCC variants.

RESULTS

Histopathological BCC and normal histological features were clearly recognizable on the OCT images. The pathological BCC features observed in the OCT images correlated with those found in the H&E-stained sections. Seven participants completed the test. The correct answer rates of the residents, fellows, and pathologists were 71%, 68%, and 83% for BCC and 44%, 57%, and 57% for the BCC subtypes, respectively.

CONCLUSION

All the participants identified BCC in >70% cases with a learning time of only 13 minutes. The results indicated that cellular-resolution OCT provided high-quality images similar to the conventional pathology slides. Pathology experience did reflect the diagnostic accuracy. However, a longer training time is still needed at all levels to recognize the BCC subtypes correctly.

A DIC-Based Study on Compressive Responses of Concrete after Exposure to Elevated Temperatures

This paper provides an experimental investigation on the cracking process and residual mechanical properties of concrete after exposure to elevated temperatures. A total of 36 standard concrete prism specimens were tested after exposure to high temperatures of up to 600 °C. The failure modes, cracking process, residual mechanical properties, deformation characteristics and the strain distribution on the surface during the loading procedure were presented. The influences of exposure temperature and water–cement ratio (w/c) were interpreted. The digital image correlation (DIC) method was applied to quantitatively and visually characterize the development of cracking and relative displacement on the concrete surface. The findings suggest that the residual compressive strength and elastic modulus of the concrete decreases gradually with the increasing temperature, especially in the specimens with lower w/c ratio. The DIC technique provides an effective means to measure very precise and detailed information, including the crack opening and distribution of strain on the concrete surface.

No Useful Field Expansion with Full-field Prisms

SIGNIFICANCE

Full-field prisms that fill the entire spectacle eye wire have been considered as field expansion devices for homonymous hemianopia (HH) and acquired monocular vision (AMV). Although the full-field prism is used for addressing binocular dysfunction and for prism adaptation training after brain injury as treatment for spatial hemineglect, we show that the full-field prism for field expansion does not effectively expand the visual field in either HH or AMV.

PURPOSE

Full-field prisms may shift a portion of the blind side to the residual seeing side. However, foveal fixation on an object of interest through a full-field prism requires head and/or eye rotation away from the blind side, thus negating the shift of the field toward the blind side.

METHODS

We fit meniscus and flat full-field 7Δ and 12Δ yoked prisms and conducted Goldmann perimetry in HH and AMV. We compared the perimetry results with ray tracing calculations.

RESULTS

The rated prism power was in effect at the primary position of gaze for all prisms, and the meniscus prisms maintained almost constant power at all eccentricities. To fixate on the perimetry target, the subjects needed to turn their head and/or eyes away from the blind side, which negated the field shift into the blind side. In HH, there was no difference in the perimetry results on the blind side with any of the prisms. In AMV, the lower nasal field of view was slightly shifted into the blind side with the flat prisms, but not with the meniscus prisms.

CONCLUSIONS

Full-field prisms are not an effective field expansion device owing to the inevitable fixation shift. There is potential for a small field shift with the flat full-field prism in AMV, but such lenses cannot incorporate refractive correction. Furthermore, in considering the apical scotoma, the shift provides a mere field substitution at best.

In vivo full-field functional optical hemocytometer

We present an in vivo lab-free full-field functional optical hemocytometer (FFOH) for application to the capillaries of a live biological specimen, based on the absorption intensity fluctuation modulation (AIFM) effect. Because of the absorption difference between the red blood cells (RBCs) and background tissue under low-coherence light illumination, an endogenous instantaneous intensity fluctuation is generated by the AIFM effect when RBCs discontinuously traverse the capillary. The AIFM effect is used to highlight the RBC signal relative to the background tissue by computing the real-time modulation depth. FFOH can simultaneously provide a flow video, the flow velocity and the RBC count. Ourexperimental results can potentially be applied to study the physiological mechanisms of the blood circulation systems of near-transparent live biological samples.

Recovering vector displacement estimates in quasistatic elastography using sparse relaxation of the momentum equation

We consider the problem of estimating the 2D vector displacement field in a heterogeneous elastic solid deforming under plane stress conditions. The problem is motivated by applications in quasistatic elastography. From precise and accurate measurements of one component of the 2D vector displacement field and very limited information of the second component, the method reconstructs the second component quite accurately. No a priori knowledge of the heterogeneous distribution of material properties is required. This method relies on using a special form of the momentum equations to filter ultrasound displacement measurements to produce more precise estimates. We verify the method with applications to simulated displacement data. We validate the method with applications to displacement data measured from a tissue mimicking phantom, and in-vivo data; significant improvements are noticed in the filtered displacements recovered from all the tests. In verification studies, error in lateral displacement estimates decreased from about 50% to about 2%, and strain error decreased from more than 250% to below 2%.

Image stack alignment in full-field X-ray absorption spectroscopy using SIFT_PyOCL

Full-field X-ray absorption spectroscopy experiments allow the acquisition of millions of spectra within minutes. However, the construction of the hyperspectral image requires an image alignment procedure with sub-pixel precision. While the image correlation algorithm has originally been used for image re-alignment using translations, the Scale Invariant Feature Transform (SIFT) algorithm (which is by design robust versus rotation, illumination change, translation and scaling) presents an additional advantage: the alignment can be limited to a region of interest of any arbitrary shape. In this context, a Python module, named SIFT_PyOCL, has been developed. It implements a parallel version of the SIFT algorithm in OpenCL, providing high-speed image registration and alignment both on processors and graphics cards. The performance of the algorithm allows online processing of large datasets.

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available.