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.

/pdf/txm-wizard-a-program-for-advanced-data-collection-and-5e7z1f5n24.pdf

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

Purpose: The edge illumination (EI) x-ray phase contrast imaging (XPCi) method has been recently further developed to perform tomographic and, thus, volumetric imaging. In this paper, the first tomographic EI XPCi images acquired with a conventional x-ray source at dose levels below that used for preclinical small animal imaging are presented. Methods: Two test objects, a biological sample and a custom-built phantom, were imaged with a laboratory-based EI XPCi setup in tomography mode. Tomographic maps that show the phase shift and attenuating properties of the object were reconstructed, and analyzed in terms of signal-to-noise ratio and quantitative accuracy. Dose measurements using thermoluminescence devices were performed. Results: The obtained images demonstrate that phase based imaging methods can provide superior results compared to attenuation based modalities for weakly attenuating samples also in 3D. Moreover, and, most importantly, they demonstrate the feasibility of low-dose imaging. In addition, the experimental results can be considered quantitative within the constraints imposed by polychromaticity. Conclusions: The results, together with the method's dose efficiency and compatibility with conventional x-ray sources, indicate that tomographic EI XPCi can become an important tool for the routine imaging of biomedical samples.

https://aapm.onlinelibrary.wiley.com/doi/epdf/10.1118/1.4884297

Low-dose phase contrast tomography with conventional x-ray sources

Purpose: The noise variance versus spatial resolution relationship in differential phase contrast (DPC) projection imaging and computed tomography (CT) are derived and compared to conventional absorption-based x-ray projection imaging and CT.

Methods: The scaling law for DPC-CT is theoretically derived and subsequently validated with phantom results from an experimental Talbot–Lau interferometer system.

Results: For the DPC imaging method, the noise variance in the differential projection images follows the same inverse-square law with spatial resolution as in conventional absorption-based x-ray imaging projections. However, both in theory and experimental results, in DPC-CT the noise variance scales with spatial resolution following an inverse linear relationship with fixed slice thickness.

Conclusions: The scaling law in DPC-CT implies a lesser noise, and therefore dose, penalty for moving to higher spatial resolutions when compared to conventional absorption-based CT in order to maintain the same contrast-to-noise ratio.

/pdf/scaling-law-for-noise-variance-and-spatial-resolution-in-tu3jsgk3yz.pdf

Scaling law for noise variance and spatial resolution in differential phase contrast computed tomography

Ever since the first demonstration of phase contrast imaging (PCI) in the 1930s by Frits Zernike, people have realized the significant advantage of phase contrast over conventional absorption-based imaging in terms of sensitivity to ‘transparent’ features within specimens. Thus, x-ray phase contrast imaging (XPCI) holds great potential in studies of soft biological tissues, typically containing low Z elements such as C, H, O and N. Particularly when synchrotron hard x-rays are employed, the favourable brightness, energy tunability, monochromatic characteristics and penetration depth have dramatically enhanced the quality and variety of XPCI methods, which permit detection of the phase shift associated with 3D geometry of relatively large samples in a non-destructive manner. In this paper, we review recent advances in several synchrotron-based hard x-ray XPCI methods. Challenges and key factors in methodological development are discussed, and biological and medical applications are presented.

http://iopscience.iop.org/article/10.1088/0022-3727/46/49/494001/pdf

Recent advances in synchrotron-based hard x-ray phase contrast imaging

Phase-based approaches can revolutionize X-ray imaging and remove its main limitation: poor image contrast arising from low attenuation differences. They exploit the unit decrement of the real part of the refractive index, typically 1000 times larger than the imaginary part driving attenuation. This increases the contrast of all details, and enables the detection of features classically considered “X-ray invisible”. Following pioneering experiments dating back to the mid-sixties, X-ray phase contrast imaging “exploded” in the mid-nineties, when third generation synchrotron sources became more widely available. Applications were proposed in fields as diverse as material science, palaeontology, biology, food science, cultural heritage preservation, and many others. Among these applications, medicine has been constantly considered the most important; among medical applications, mammography is arguably the one that attracted most attention. Applications to mammography were pioneered by the SYRMEP (SYnchrotron Radiation for Medical Physics) group in Trieste, which was already active in the area through a combination of innovative ways to do imaging at synchrotrons and development of novel X-ray detectors. This pioneering phase led to the only clinical experience of phase contrast mammography on human patients, and spawned a number of ideas as to how these advances could be translated into clinical practice.

/pdf/x-ray-phase-contrast-imaging-from-synchrotrons-to-37o1i8cdx4.pdf

X-ray phase contrast imaging: From synchrotrons to conventional sources

X-ray diffraction enhanced imaging based on synchrotron radiation has extremely high sensitivity of weakly absorbing low-Z samples in medical and biological fields. This letter is dedicated to a direct reconstruction algorithm for directional-derivative projections of computed tomography of diffraction enhanced imaging. It is a “one-step” algorithm and does not require any restoration processing compared with the current “two-step” methods. The actual values of the sample’s refractive index decrement can be estimated from its reconstruction images directly. The algorithm is proven by the actual experiment at the Beijing Synchrotron Radiation Facility and the reconstructed images are described finally.

Ai-Min Yu

Papers

Direct computed tomographic reconstruction for directional-derivative projections of computed tomography of diffraction enhanced imaging