Phase contrast micro-CT with adjustable in-slice spatial resolution at constant magnification.

Objective.To report on a micro computed tomography (micro-CT) system capable of x-ray phase contrast imaging and of increasing spatial resolution at constant magnification.Approach.The micro-CT system implements the edge illumination (EI) method, which relies on two absorbing masks with periodically spaced transmitting apertures in the beam path; these split the beam into an array of beamlets and provide sensitivity to the beamlets' directionality, i.e. refraction. In EI, spatial resolution depends on the width of the beamlets rather than on the source/detector point spread function (PSF), meaning that resolution can be increased by decreasing the mask apertures, without changing the source/detector PSF or the magnification.Main results.We have designed a dedicated mask featuring multiple bands with differently sized apertures and used this to demonstrate that resolution is a tuneable parameter in our system, by showing that increasingly small apertures deliver increasingly detailed images. Phase contrast images of a bar pattern-based resolution phantom and a biological sample (a mouse embryo) were obtained at multiple resolutions.Significance.The new micro-CT system could find application in areas where phase contrast is already known to provide superior image quality, while the added tuneable resolution functionality could enable more sophisticated analyses in these applications, e.g. by scanning samples at multiple scales.

Cycloidal CT with CNN-based sinogram completion and in-scan generation of training data.

In x-ray computed tomography (CT), the achievable image resolution is typically limited by several pre-fixed characteristics of the x-ray source and detector. Structuring the x-ray beam using a mask with alternating opaque and transmitting septa can overcome this limit. However, the use of a mask imposes an undersampling problem: to obtain complete datasets, significant lateral sample stepping is needed in addition to the sample rotation, resulting in high x-ray doses and long acquisition times. Cycloidal CT, an alternative scanning scheme by which the sample is rotated and translated simultaneously, can provide high aperture-driven resolution without sample stepping, resulting in a lower radiation dose and faster scans. However, cycloidal sinograms are incomplete and must be restored before tomographic images can be computed. In this work, we demonstrate that high-quality images can be reconstructed by applying the recently proposed Mixed Scale Dense (MS-D) convolutional neural network (CNN) to this task. We also propose a novel training approach by which training data are acquired as part of each scan, thus removing the need for large sets of pre-existing reference data, the acquisition of which is often not practicable or possible. We present results for both simulated datasets and real-world data, showing that the combination of cycloidal CT and machine learning-based data recovery can lead to accurate high-resolution images at a limited dose.

Retrieval of weak x-ray scattering using edge illumination.

X-ray phase contrast imaging provides additional modes of image contrast compared to conventional attenuation-based x-ray imaging, thus providing additional structural and functional information about the sample. The edge-illumination (EI) technique has been used to provide attenuation, refraction, and scattering contrast in both biological and non-biological samples. However, the retrieval of low scattering signals by fitting a single Gaussian remains problematic, principally due to the inability of the EI system to achieve perfect dark-field illumination. We present a new retrieval method that fits three Gaussians, which successfully overcomes this limitation, and provide examples of the retrieval of such signals in highly absorbing, weakly scattering samples.

Development of a reliable and reproducible phantom manufacturing method using silica microspheres in silicone.

Optically scattering phantoms composed of silica microspheres embedded in an optically clear silicone matrix were manufactured using a previously developed method. Multiple problems, such as sphere aggregation, adsorption to the cast, and silicone shrinkage, were, however, frequently encountered. Solutions to these problems were developed and an improved method, incorporating these solutions, is presented. The improved method offers excellent reliability and reproducibility for creating phantoms with uniform scattering coefficient. We also present evidence of decreased sphere aggregation.