SYnchrotron Radiation For MEdical Physics Research Articles

Autofinding egg parasitoids in moth eggs by using machine learning methods in synchrotron-coherent X-ray imaging

The use of a non-destructive technique, such as the propagation-based X-ray phase contrast radiography (PBR) can be an innovative method for automatic parasitism analysis, especially if it presents standard structures. Herein, an artificial intelligence (AI) model is applied in order to establish a computer vision of egg parasitoids in PBRs of parasitized moth eggs acquired at the Synchrotron Radiation for Medical Physics (SYRMEP) beamline at ELETTRA. PBRs of eggs parasitized in four different stages of parasitism (0 days, 3 days, 5 days and 7 days) have been tested. The AI model performance was evaluated by using different metrics. Average Precision (AP), which measures the accuracy of object detection, was found to be 0.866 and 0.741 for the moth eggs and for the parasites, respectively. Additionally, we found that as stage of parasitism becomes longer, the accuracy of parasitism detection also increases (76 % at 7 days).

Multiscale biomedical imaging at the SYRMEP beamline of Elettra - Closing the gap between preclinical research and patient applications

Here we present the specifications and capabilities of the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline of the Italian Synchrotron “Elettra” in Trieste. SYRMEP was designed to provide X-ray imaging in an energy range that fits both biomedical research and clinical applications on patients. Additionally, SYRMEP covers a spatial resolution range of 100 μm down to 1 μm (1/50th the width of a human hair) with a comparably wide field-of-view (FOV), which enables studies in large specimens and therefore closes the gap between micro computed tomography (CT) in biomedical research and clinical CT imaging. Moreover, the possible long sample-to-detector distance allows for an effective use of free-propagation phase contrast that increases dose efficacy and soft-tissue contrast. These parameters and their function are further discussed on a set of examples of biomedical applications.

Medical Applications of Tissue-Equivalent, Organic-Based Flexible Direct X-Ray Detectors

The aim of this study is to assess direct X-ray detectors based on organic thin films, fabricated onto flexible plastic substrates and operating at ultra-low bias (<1 V), for different medical applications. With this purpose, flexible fully organic pixelated X-ray detectors have been tested at the imaging beamline SYRMEP (SYnchrotron Radiation for MEdical Physics) at the Italian synchrotron Elettra, Trieste. The detectors’ performance has been assessed for potential employment both as reliable wearable personal dosimeters for patients and as flexible X-ray medical imaging systems. A spatial resolution of 1.4 lp mm-1 with a contrast of 0.37 has been evaluated. Finally, we validate the detector using X-ray doses and energies typically employed for actual medical radiography, and using X-ray beam pulses provided by a commercial dental radiography system, recording a sensitivity of 1.6×105 µC Gy-1 cm-3 with a linear response with increasing of the dose rates and a reliable signal to 100 ms X-rays pulses.

Quantitative pore network analysis and permeability evaluation of porous carbonate reservoir rocks using X-ray computed microtomography images

The texture and the morphology of the pore network exerts a primary control in the fluid storage and migration of geofluids within porous carbonates reservoirs. The architecture of the pore network of porous carbonates are highly variable because of primary depositional settings, diagenesis processes and deformation. This issue represents an important challenge for the characterization and exploitation plan of this type of reservoirs in different industries such as, hydrocarbon, ground water and geothermal energy. This type of rocks is widely studied because they represent important reservoirs for geofluids around the globe. However, there are few studies assessing the control exerted by the pore network properties (e.g. porosity, pore size distribution, connectivity, tortuosity) on the permeability. In this work the control exerted by the pore network on the storage and migration capacity in porous carbonates is evaluated by combining synchrotron X-ray computed microtomography (SR micro-CT) and computational fluid dynamics. The studied rock samples are mainly porous grainstones exposed in south and central Italy. Some samples may content deformation structures (i.e. deformation bands) or may be altered by diagenesis. Previous studies have reported permeability differences and significant variability of the in-situ hydrocarbon distribution in the studied rocks. The SR micro-CT imaging experiments were performed at the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline (Elettra-Sincrotrone Trieste laboratory, Italy). This beamline was suitable for studying the rocks samples due to its nearly-parallel geometry and a high spatial coherence allowing the phase contrast effects to enhance the visibility of objects with similar linear attenuation coefficients. In this study, the selected spatial resolution of the images is variable (1.0-9.0 μm) depending on the grain size distribution of the rock sample. The SR micro-CT images were used for both performing a quantitative pore network analysis of the studied rock samples and performing computational fluid dynamics experiments. These experiments consist in simulating a pressure-driven flow by using the lattice-Boltzmann method (LBM) with multiple relaxation time (MRT) approach. This method generates viscosity-independent results of permeability. The permeability of the volume was calculated using Darcy’s law once steady conditions were reached. To evaluate isotropy, the results of permeability and the pore network properties were calculated in three dimensions. The results indicate that deformation and diagenetic processes may have and important impact on the pore network properties and therefore on storage (porosity) and migration (permeability) capacity of the studied rocks.

Synchrotron microtomography to evaluate effects of different polychemotherapy drugs on cortical bone structure

Purpose: To determine the effects of different polychemotherapy drugs on cortical bone structure, the femur diaphysis of rats were treated with two different chemotherapy drugs, AC (doxorubicin + cyclophosphamide) and TC (docetaxel + cyclophosphamide), and evaluated by 3D morphological analysis using synchrotron radiation microtomography.Materials and methods: Wistar rats were classified into three groups. One group received doses of docetaxel and cyclophosphamide (G1) – TC regimen; a second group received doses of doxorubicin and cyclophosphamide (G2) – AC regimen; while a control group (G0) received no further treatment. 3D tomographic images of the rats’ femurs were obtained at the SYRMEP (Synchrotron Radiation for Medical Physics) beamline at the ELETTRA Synchrotron Laboratory in Trieste, Italy, using monochromatic X-rays with resolution of 9 μm.Results: It could be shown that the treatment caused significant differences in morphological parameters measured from the 3D images of femur diaphysis of rats, among the studied groups, complementing a previous study using stereological methods, biochemistry and electron microscopy.Conclusions: Our results indicate that the same process of osteoporosis caused by advancing age might occur in young women treated with docetaxel + cyclophosphamide (TC) and doxorubicin + cyclophosphamide (AC). 3D microtomography was shown to be an outstanding technique for bone analysis.

Analysis of cortical bone porosity using synchrotron radiation microtomography to evaluate the effects of chemotherapy

Abstract Microporosities play important biologic and mechanical roles on health. One of the side effects caused by some chemotherapy drugs is the induction of amenorrhea, temporary or not, in premenopausal women, with a consequent decrease in estrogen production, which can lead to cortical bone changes. In the present work, the femur diaphysis of rats treated with chemotherapy drugs were evaluated by 3D morphometric parameters using synchrotron radiation microtomography. Control animals were also evaluated for comparison. The 3D tomographic images were obtained at the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline at the ELETTRA Synchrotron Laboratory in Trieste, Italy. Results showed significant differences in morphometric parameters measured from the 3D images of femur diaphysis of rats.

Synchrotron based planar imaging and digital tomosynthesis of breast and biopsy phantoms using a CMOS active pixel sensor

The SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline at Elettra is performing the first mammography study on human patients using free-space propagation phase contrast imaging. The stricter spatial resolution requirements of this method currently force the use of conventional films or specialized computed radiography (CR) systems. This also prevents the implementation of three-dimensional (3D) approaches. This paper explores the use of an X-ray detector based on complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) technology as a possible alternative, for acquisitions both in planar and tomosynthesis geometry.Results indicate higher quality of the images acquired with the synchrotron set-up in both geometries. This improvement can be partly ascribed to the use of parallel, collimated and monochromatic synchrotron radiation (resulting in scatter rejection, no penumbra-induced blurring and optimized X-ray energy), and partly to phase contrast effects. Even though the pixel size of the used detector is still too large – and thus suboptimal – for free-space propagation phase contrast imaging, a degree of phase-induced edge enhancement can clearly be observed in the images.

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

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.

Synchrotron radiation X-ray microtomography and histomorphometry for evaluation of chemotherapy effects in trabecular bone structure

Three-dimensional microtomography has the potential to examine complete bones of small laboratory animals with very high resolution in a non-invasive way. One of the side effects caused by some chemotherapy drugs is the induction of amenorrhea, temporary or not, in premenopausal women, with a consequent decrease in estrogen production, which can lead to bone changes. In the present work, the femur heads of rats treated with chemotherapy drugs were evaluated by 3D histomorphometry using synchrotron radiation microcomputed tomography. Control animals were also evaluated for comparison. The 3D tomographic images were obtained at the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline at the Elettra Synchrotron Laboratory in Trieste, Italy. Results showed significant differences in morphometric parameters measured from the 3D images of femur heads of rats in both analyzed groups.

First application of computed radiology to mammography with synchrotron radiation

The aim of this study was to evaluate the feasibility of phase-contrast mammography with synchrotron radiation using a high-resolution computed radiology (CR) system devoted to mammography. The study was performed at the Synchrotron Radiation for Medical Physics (SYRMEP) beamline of the Elettra synchrotron radiation (SR) facility in Trieste (Italy); X-ray beams were in the range 16-22 keV with a high degree of monochromaticity and spatial coherence. The CR system evaluated is the FCR Profect CS by Fujifilm Global. The first images were obtained from test objects and surgical breast specimens. Images obtained using SR and both screen-film and the CR system were compared with images of the same samples acquired with digital mammography equipment. In view of the good quality of the results obtained, the CR system was used in two mammographic examinations with SR. Images acquired using SR and both screen-film and CR were obtained with the same level of delivered dose. Image quality obtained with CR was similar or superior to that of screen-film images. Moreover, the digital images obtained with SR were always better than those acquired using the digital mammography system. Phase-contrast mammography with SR using the studied CR system is a feasible option.

Preliminary analysis of radiation dose effects to rat femora microstructure using synchrotron radiation computed microtomography

In this work we investigated the consequences of irradiation in the femur of rats to a radiation dose of 5 Gy. Three different sites in femur specimens were imaged using synchrotron radiation microcomputed tomography to assess trabecular bone microarchitecture: head, distal metaphysis and distal epiphysis. Histomorphometric quantification was extracted directly from the 3D tomographic images using synchrontron radiation. The 3D tomographic images were obtained at the SYnchrotron Radiation for MEdical Physics (SYRMEP) beamline at the Elettra Synchrotron Laboratory in Trieste, Italy. A better understanding of the biological interactions that occur after exposure to photon radiation is needed in order to optimize therapeutic regimens and facilitate development and strategies that decrease radiation-induced side effects in humans. Results showed significant differences between irradiated and non-irradiated mostly in head and distal metaphysis bone sites. Key words: Radiotherapy, microtomography, synchrotron radiation, dose effects, histomorphometry, bone microstructure.

Automated segmentation of synchrotron radiation micro-computed tomography biomedical images using Graph Cuts and neural networks

Synchrotron Radiation (SR) X-ray micro-Computed Tomography (μCT) enables magnified images to be used as a non-invasive and non-destructive technique with a high space resolution for the qualitative and quantitative analyses of biomedical samples. The research on applications of segmentation algorithms to SR-μCT is an open problem, due to the interesting and well-known characteristics of SR images for visualization, such as the high resolution and the phase contrast effect. In this article, we describe and assess the application of the Energy Minimization via Graph Cuts (EMvGC) algorithm for the segmentation of SR-μCT biomedical images acquired at the Synchrotron Radiation for MEdical Physics (SYRMEP) beam line at the Elettra Laboratory (Trieste, Italy). We also propose a method using EMvGC with Artificial Neural Networks (EMANNs) for correcting misclassifications due to intensity variation of phase contrast, which are important effects and sometimes indispensable in certain biomedical applications, although they impair the segmentation provided by conventional techniques. Results demonstrate considerable success in the segmentation of SR-μCT biomedical images, with average Dice Similarity Coefficient 99.88% for bony tissue in Wistar Rats rib samples (EMvGC), as well as 98.95% and 98.02% for scans of Rhodnius prolixus insect samples (Chagas's disease vector) with EMANNs, in relation to manual segmentation. The techniques EMvGC and EMANNs cope with the task of performing segmentation in images with the intensity variation due to phase contrast effects, presenting a superior performance in comparison to conventional segmentation techniques based on thresholding and linear/nonlinear image filtering, which is also discussed in the present article.

Phase-Contrast Mammography at the SYRMEP Beamline of Elettra

At the SYnchrotron Radiation for MEdical Physics (SYRMEP) beamline of Elettra, a widespread research activity in bio-medical imaging has been developed since 1997 [1]. The core program carried out by the SYRMEP research team concerns the use of synchrotron radiation (SR) for mammography in the effort of improving image diagnostic quality innovating the imaging technique and the detection system.

Breast computed tomography with the PICASSO detector: A feasibility study

The SYRMEP (Synchrotron Radiation for Medical Physics) collaboration has performed, for the first time in the world, a clinical program of mammography with synchrotron radiation. This program provided excellent results, although utilizing a commercial screen-film system as a detector. The PICASSO (Phase Imaging for Clinical Application with Silicon detector and Synchrotron radiation) project has developed a detector prototype capable of fully exploiting the peculiar characteristics of the synchrotron source, utilizing silicon microstrip sensors illuminated in the edge-on geometry and operated in single-photon counting. In this paper the potential of the PICASSO detector in breast computed tomography was evaluated by means of custom phantoms. Very encouraging results have been obtained with severe dose constrains as far as both spatial and contrast resolution are concerned. Moreover, the capability of detecting phase contrast effects was demonstrated, albeit with a higher delivered dose.

3D histomorphometric quantification of trabecular bones by computed microtomography using synchrotron radiation

Conventional bone histomorphometry is an important method for quantitative evaluation of bone microstructure. X-ray computed microtomography is a non-invasive technique, which can be used to evaluate histomorphometric indices in trabecular bones (BV/TV, BS/BV, Tb.N, Tb.Th, Tb.Sp). In this technique, 3D images are used to quantify the whole sample, differently from the conventional one, in which the quantification is performed in 2D slices and extrapolated for 3D case. In this work, histomorphometric quantification using synchrotron 3D X-ray computed microtomography was performed to quantify the bone structure at different skeletal sites as well as to investigate the effects of bone diseases on quantitative understanding of bone architecture. The images were obtained at Synchrotron Radiation for MEdical Physics (SYRMEP) beamline, at ELETTRA synchrotron radiation facility, Italy. Concerning the obtained results for normal and pathological bones from same skeletal sites and individuals, from our results, a certain declining bone volume fraction was achieved. The results obtained could be used in forming the basis for comparison of the bone microarchitecture and can be a valuable tool for predicting bone fragility.

Evaluation of charge -sharing effects on the spatial resolution of the PICASSO detector

A double -layer “edge-on” silicon microstrip detector has been designed and realized in the frame of the PICASSO (Phase Imaging for Clinical Application with Silicon detector and Synchrotron radiatiOn) project at the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline of Elettra (Trieste, Italy). The detector meets the requirements for synchrotron radiation mammography with patients inregarding: (a) size, since it covers the full beam width (210 mm); (b) spatial resolution, determined by the 0.05 mm strip pitch; (c) single-photon counting capabilities, because it is able to handle more than 10 6 photons/(pixel×s); (d) contrast resolution, thanks to a threshold trim DAC that equalizes the channel sensitivity; (e) efficiency, due to the high absorption in the 15–20 mm sensor depth. Experimental measurements evidence charge sharing, though not compromising the spatial resolution.

A single-photon counting “edge-on” silicon detector for synchrotron radiation mammography

The Phase Imaging for Clinical Application with Silicon detector and Synchrotron radiatiOn (PICASSO) project is developing an “edge-on” silicon microstrip detector for mammography with synchrotron radiation. The sensor is equipped with a fast single-photon counting electronics based on the Mythen-II application-specific integrated circuit. A first prototype has been assembled and tested at the SYnchrotron Radiation for MEdical Physics (SYRMEP) beamline at Elettra in Trieste, Italy. The first results are presented in this study including evidence of high-rate single-photon counting with negligible losses up to 1.2×10 6 incident photons per pixel per second; spatial resolution consistent with the pixel aperture (0.3 mm×0.05 mm); high-quality imaging of test-objects, obtained with a dose comparable to the one delivered in modern full-field digital mammographic systems.

Quantitative evaluation of bone-mineral density loss using X-ray coherent scattering

In this work, we intend to relate the mineral to non-mineral bone scattering intensity ratio with the bone-mineral density (BMD) reduction. In this way, EDXRD can be a novel technique to measure BMD loss in function of the mineral and non-mineral scattering intensity. The scattering profiles were obtained at Laboratório Nacional de Luz Síncrotron (LNLS) at the X-ray diffraction beamline XD2. A double-crystal Si(1 1 1) pre-monochromator, upstream of the beamline, was used to select a small energy bandwidth (Δ λ/ λ≈10 −4) at 11 keV. The sample holder has a circle depression in the center to contain a range of bone and fat mixture ratios. The mixture consists of powdered cortical bone and fat, which together simulate in vivo bone. The diffraction patterns were carried out with 0.5 mm slits after and behind of the sample holder. The data were collected in 0.05° increments every 0.5 s. EDXRD results show an indication of different bone densities may be distinguished which suggested that X-ray coherent scattering technique may have a role in monitoring changes in BMD via changes in the related scattering intensity of mineral and non-mineral bone. The main aim of the Synchrotron Radiation for MEdical Physics (SYRMEP) project at the ELETTRA is the investigation and the development of innovative techniques for medical imaging. The beamline provides, at a distance of about 23 m from the source, a monochromatic, laminar section X-ray beam with a maximum area of about 160×5 mm 2 at 20 keV. The monochromator, that covers the entire angular acceptance of the beamline, is based on a double-Si (1 1 1) crystal system working in Bragg configuration. A micrometric vertical and horizontal translation stage allows the positioning and scanning of the sample with respect to the stationary beam. In this case, the detector is kept stationary in front of the beam, while the object is rotated in discrete steps in front of it. At each rotation, a projection is acquired. A goniometric double-cradle system is used to adjust the rotation axis, which must be orthogonal with respect to the detector plane in transmission computed tomography (CT). The samples consisted of a 8 mm cube of bovine bone surrounded of a cartilage interface. High-resolution images of the trabecular structure were obtained by means a 16-bit CCD camera, 2048×2048 pixels, 14 μm pixel size (maximum spatial resolution: 25 μm).

Clinical mammography at the SYRMEP beam line

The synchrotron radiation (SR) clinical mammography, using as detector a commercial screen-film system, is a further crucial step of the SYRMEP (Synchrotron Radiation for Medical Physics) Project. In March and April of this year, mammographic examinations on nine patients have been carried out with X-rays from ELETTRA, the SR laboratory in Trieste, Italy. The facility for Phase Contrast (PhC) SR mammography is now operative in patient mode and is used for patient examinations, producing breast images in different projections. The entire procedure is automated and is able to achieve the correct exposure on the film taking into consideration the requested limits on the applied dose, as a function of the thickness and glandularity of the breast. The SR mammography shows a higher spatial resolution and contrast detail visibility, in comparison with the conventional analog or digital mammography, with a comparable or lower dose. In some cases of these first nine patients, the radiologists have clarified the ambiguity of the previous examinations. These preliminary results are encouraging and a complete evaluation of the clinical impact of the new method is in progress.

A digital detector for breast computed tomography at the SYRMEP beamline

A silicon strip detector in edge on configuration with a single photon counting read-out electronics was developed for the MATISSE (MAmmographic and Tomographic Imaging with Silicon detectors and Synchrotron radiation at Elettra) project. MATISSE is an experiment aiming at a pre-clinical phase of breast computed tomography examinations at the SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline at the Elettra synchrotron light source in Trieste (Italy). A monochromatic beam in the energy range 8–35 keV is available at SYRMEP. The MATISSE detector is side illuminated, thus allowing direct conversion of X-rays with a high efficiency. The read-out electronics operates in single photon counting mode, maximizing the contrast resolution of the images. Thanks to the characteristics of the radiation spectrum and to the high efficiency of the detector, the dose delivered in a tomographic examination results comparable to the one delivered in planar conventional mammography. Detector prototypes have been assembled and tested with promising results that will be presented in this contribution.