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Learning from our neighbours: a novel approach on sinogram completion using bin-sharing and deep learning to reconstruct high quality 4DCBCT

Inspired by the success of deep learning applications on restoration of low-dose and sparse CT images, we propose a novel method to reconstruct high-quality 4D cone-beam CT (4DCBCT) images from sparse datasets. Our approach combines the idea of 'bin-sharing' with a deep convolutional neural network (CNN) model. More specifically, for each respiratory bin, an initial estimate of the patient sinogram is obtained by taking projections from adjacent bins and performing linear interpolation. Subsequently, the estimated sinogram is propagated through a CNN that predicts a full, high-quality sinogram. Lastly, the predicted sinogram is reconstructed with traditional CBCT algorithms such as the Feldkamp, Davis and Kress (FDK) method. The CNN model, which we referred to as the Sino-Net, was trained under different loss functions. We assessed the performance of the proposed method in terms of image quality metrics (mean square error, mean absolute error, peak signal-to-noise ratio and structural similarity) and tumor motion accuracy (tumor centroid deviation with respect to the ground truth). Overall, the presented prototype model was able to substantially improve the quality of 4DCBCT images, removing most of the streak artifacts and decreasing the noise with respect to the standard FDK reconstructions. The tumor centroid deviations with respect to the ground truth predicted by our method were approximately 0.5 mm, on average (maximum deviation was approximately 2 mm). These preliminary results are promising and encourage us to further investigate the performance of our model under more challenging imaging conditions and compare it against the state-of-the-art CBCT reconstruction algorithms.

physics.med-ph↗

Trajectory planning optimization for real-time 6DOF robotic patient motion compensation

We present for the first time a general 6DoF trajectory planning method that can be used in real-time image guided radiation therapy procedures for robotic stabilization of dynamically moving tumor targets. As the radiation beam is always on during the motion compensation process, it is mandatory that the 6D correction trajectory is optimal both spatially and temporally in order to maximize radiation to the tumor and minimize unintentional irradiation of healthy tissues. Unlike prior works, which relied on motion control approaches as PID or other controllers, this work presents the concept of motion planning, where all potential 6D trajectories are searched using ultrafast optimization methods and the best trajectory is chosen. As the method formulates the problem as an objective function to be solved, it allows high flexibility in that users can optimize various performance requirements such as mechanical robot limits, patient velocities, or other aspects that must operate within certain limits in order to ensure a safe medical process.

physics.med-ph↗

Deep Learning Framework for Digital Breast Tomosynthesis Reconstruction

Digital breast tomosynthesis is rapidly replacing digital mammography as the basic x-ray technique for evaluation of the breasts. However, the sparse sampling and limited angular range gives rise to different artifacts, which manufacturers try to solve in several ways. In this study we propose an extension of the Learned Primal-Dual algorithm for digital breast tomosynthesis. The Learned Primal-Dual algorithm is a deep neural network consisting of several `reconstruction blocks', which take in raw sinogram data as the initial input, perform a forward and a backward pass by taking projections and back-projections, and use a convolutional neural network to produce an intermediate reconstruction result which is then improved further by the successive reconstruction block. We extend the architecture by providing breast thickness measurements as a mask to the neural network and allow it to learn how to use this thickness mask. We have trained the algorithm on digital phantoms and the corresponding noise-free/noisy projections, and then tested the algorithm on digital phantoms for varying level of noise. Reconstruction performance of the algorithms was compared visually, using MSE loss and Structural Similarity Index. Results indicate that the proposed algorithm outperforms the baseline iterative reconstruction algorithm in terms of reconstruction quality for both breast edges and internal structures and is robust to noise.

physics.med-ph↗

Translational Motion Compensation for Soft Tissue Velocity Images

Purpose: Advancements in MRI Tissue Phase Velocity Mapping (TPM) allow for the acquisition of higher quality velocity cardiac images providing better assessment of regional myocardial deformation for accurate disease diagnosis, pre-operative planning and post-operative patient surveillance. Translation of TPM velocities from the scanner's reference coordinate system to the regional cardiac coordinate system requires decoupling of translational motion and motion due to myocardial deformation. Despite existing techniques for respiratory motion compensation in TPM, there is still a remaining translational velocity component due to the global motion of the beating heart. To compensate for translational motion in cardiac TPM, we propose an image-processing method, which we have evaluated on synthetic data and applied on in vivo TPM data. Methods: Translational motion is estimated from a suitable region of velocities automatically defined in the left-ventricular volume. The region is generated by dilating the medial axis of myocardial masks in each slice and the translational velocity is estimated by integration in this region. The method was evaluated on synthetic data and in vivo data corrupted with a translational velocity component (200% of the maximum measured velocity). Accuracy and robustness were examined and the method was applied on 10 in vivo datasets. Results: The results from synthetic and in vivo corrupted data show excellent performance with an estimation error less than 0.3% and high robustness in both cases. The effectiveness of the method is confirmed with visual observation of results from the 10 datasets. Conclusion: The proposed method is accurate and suitable for translational motion correction of the left ventricular velocity fields. The current method for translational motion compensation could be applied to any annular contracting (tissue) structure.

physics.med-ph↗

Deep Boosted Regression for MR to CT Synthesis

Attenuation correction is an essential requirement of positron emission tomography (PET) image reconstruction to allow for accurate quantification. However, attenuation correction is particularly challenging for PET-MRI as neither PET nor magnetic resonance imaging (MRI) can directly image tissue attenuation properties. MRI-based computed tomography (CT) synthesis has been proposed as an alternative to physics based and segmentation-based approaches that assign a population-based tissue density value in order to generate an attenuation map. We propose a novel deep fully convolutional neural network that generates synthetic CTs in a recursive manner by gradually reducing the residuals of the previous network, increasing the overall accuracy and generalisability, while keeping the number of trainable parameters within reasonable limits. The model is trained on a database of 20 pre-acquired MRI/CT pairs and a four-fold random bootstrapped validation with a 80:20 split is performed. Quantitative results show that the proposed framework outperforms a state-of-the-art atlas-based approach decreasing the Mean Absolute Error (MAE) from 131HU to 68HU for the synthetic CTs and reducing the PET reconstruction error from 14.3% to 7.2%.

physics.med-ph↗

Probabilistic Graphical Modeling approach to dynamic PET direct parametric map estimation and image reconstruction

In the context of dynamic emission tomography, the conventional processing pipeline consists of independent image reconstruction of single time frames, followed by the application of a suitable kinetic model to time activity curves (TACs) at the voxel or region-of-interest level. The relatively new field of 4D PET direct reconstruction, by contrast, seeks to move beyond this scheme and incorporate information from multiple time frames within the reconstruction task. Existing 4D direct models are based on a deterministic description of voxels' TACs, captured by the chosen kinetic model, considering the photon counting process the only source of uncertainty. In this work, we introduce a new probabilistic modeling strategy based on the key assumption that activity time course would be subject to uncertainty even if the parameters of the underlying dynamic process were known. This leads to a hierarchical Bayesian model, which we formulate using the formalism of Probabilistic Graphical Modeling (PGM). The inference of the joint probability density function arising from PGM is addressed using a new gradient-based iterative algorithm, which presents several advantages compared to existing direct methods: it is flexible to an arbitrary choice of linear and nonlinear kinetic model; it enables the inclusion of arbitrary (sub)differentiable priors for parametric maps; it is simpler to implement and suitable to integration in computing frameworks for machine learning. Computer simulations and an application to real patient scan showed how the proposed approach allows us to weight the importance of the kinetic model, providing a bridge between indirect and deterministic direct methods.

stat.AP↗

High fidelity fibre-based physiological sensing deep in tissue

Physiological sensing deep in tissue, remains a clinical challenge. Here a flexible miniaturised sensing optrode providing a platform to perform minimally invasive in vivo in situ measurements is reported. Silica microspheres covalently coupled with a high density of ratiometrically configured fluorophores were deposited into etched pits on the distal end of a 150 micron diameter multicore optical fibre. With this platform, multiplexed photonic measurements of pH and oxygen concentration with high precision in the distal alveolar space of the lung is reported. We demonstrated the phenomenon that high-density deposition of carboxyfluorescein covalently coupled to silica microspheres shows an inverse shift in fluorescence in response to varying pH. This platform delivered fast and accurate measurements, near instantaneous response time, no photobleaching, immunity to power fluctuations and a flexible architecture for addition of multiple sensors.

physics.med-ph↗

DeepCEST: 9.4 T Chemical Exchange Saturation Transfer MRI contrast predicted from 3 T data - a proof of concept study

Purpose: Separation of different CEST signals in the Z-spectrum is a challenge especially at low field strengths where amide, amine, and NOE peaks coalesce with each other or with the water peak. The purpose of this work is to investigate if the information in 3T spectra can be extracted by a deep learning approach trained by 9.4T human brain target data. Methods: Highly-spectrally-resolved Z-spectra from the same volunteer were acquired by 3D-snapshot CEST MRI at 3 T and 9.4 T with similar saturation schemes. The volume-registered 3 T Z-spectra-stack was then used as input data for a 3-layer deep neural network with the volume-registered 9.4 T fitted parameter stack as target data. The neural network was optimized and applied to training data, to unseen data from a different volunteer, and as well to a tumor patient data set. Results: A useful neural net architecture could be found and verified in healthy volunteers. The principle gray-/white matter contrast of the different CEST effects was predicted with only small deviations. The 9.4 T prediction was less noisy compared to the directly measured CEST maps, however at the cost of slightly lower tissue contrast. Application to a tumor patient measured at 3 T and 9.4 T revealed that tumorous tissue Z-spectra and corresponding hyper/hypo-intensities of different CEST effects can also be predicted. Conclusion: Deep learning might be a powerful tool for CEST data processing and deepCEST could bring the benefits and insights of the few ultra-high field sites to a broader clinical use. Vice versa deepCEST might help for determining which subjects are good candidates to measure additionally at UHF.

physics.med-ph↗

Tomographic X-ray data of 3D cross phantom

This is the documentation of the tomographic X-ray data of cross phantom made available at this https URL The data can be freely used for scientific purposes with appropriate references to the data and to this document in arxiv.org. The data set consists of (1) the X-ray sinogram with 16 or 30 time frames (depending on theresolution) of 2D slices of the phantom and (2) the corresponding static and dynamic measurement matrices modeling the linear operation of the X-ray transform. Each of these sinograms was obtained from a measured 360-projection fan-beam sinogram by down-sampling and taking logarithms. The original (measured) sinogram is also provided in its original form and resolution.

physics.med-ph↗

High-speed dual color fluorescence lifetime endomicroscopy for highly-multiplexed pulmonary diagnostic applications and detection of labeled bacteria

We present a dual color laser scanning endomicroscope capable of fluorescence lifetime endomicroscopy at one frame per second (FPS). The scanning system uses a coherent imaging fiber with 30,000 cores. High-speed lifetime imaging is achieved by distributing the signal over an array of 1024 parallel single-photon avalanche photo--diode detectors (SPADs), minimizing detection dead time maximizing the number of photons detected per excitation pulse without photon pile--up to achieve the high frame rate. Dual color fluorescence imaging is achieved by temporally shifting the dual excitation lasers, with respect to each other, to separate the two spectrally distinct fluorescent decays. Combining the temporal encoding, to provide spectral separation, with lifetime measurements we show a one FPS, multi-channel endomicroscopy platform for clinical applications and diagnosis. We demonstrate the potential of the system by imaging smartprobe-labeled bacteria in ex vivo samples of human lung using lifetime to differentiate bacterial fluorescence from the strong background lung auto--fluorescence which was used to provide structural information.

physics.med-ph↗

A method to optimize patient specific HU-SP calibration curve from proton range measurements

Proton radiotherapy promises accurate dose delivery to a tumor and minimal dose deposition to all other tissues. However, in practice the planned dose distribution may not conform to the actual one due to noisy data and different types of errors. One such error comes in a form of potentially inaccurate conversion of the Hounsfield units (HU) to stopping powers (SP) of protons. We propose a method of improving the CC based on a planning CT and proton range measurements acquired during treatment. The range data were simulated using a virtual CC and a planning CT. The range data were given two types of noise: range shift due to patient setup errors; and range noise due to measurement imprecision, including a misalignment of the range measuring device. The method consists of two parts. The first part involves a Taylor expansion of the water equivalent path length (WEPL) map in terms of the range shift caused by the difference between the planning and the virtual CC. The range shift is then solved for explicitly, leading to a polynomial function of the difference between the two CCs. The second part consists in minimizing a score function relating the range due to the virtual CC and the range due to the optimized CC. Tested on ten different CCs, our results show that, with range data collected over a few fractions (less than 10), the optimized CC leads to an overall reduction of the range difference. More precisely, on average, the uncertainty of the CC was reduced from 2.67% to 1.62%, while the average reduction of the WEPL bias was reduced from 2.14% to 0.74%. The advantage of our method over others is 1) its speed, and 2) the fact that the range data it necessitates are acquired during the treatment itself, and as such it does not burden the patient with additional dose.

physics.med-ph↗

Functional imaging of ganglion and receptor cells in living human retina by osmotic contrast

Imaging neuronal activity non-invasively in vivo is of tremendous interest, but current imaging techniques lack either functional contrast or necessary microscopic resolution. The retina is the only part of the central nervous system (CNS) that allows us direct optical access. Not only ophthalmic diseases, but also many degenerative disorders of the CNS go along with pathological changes in the retina. Consequently, functional analysis of retinal neurons could lead to an earlier and better diagnosis and understanding of those diseases. Recently, we showed that an activation of photoreceptor cells could be visualized in humans using a phase sensitive evaluation of optical coherence tomography data. The optical path length of the outer segments changes by a few hundred nanometers in response to optical stimulation. Here, we show simultaneous imaging of the activation of photoreceptor and ganglion cells. The signals from the ganglion cells are ten-fold smaller than those from the photoreceptor cells and were only visible using new algorithms for suppressing motion artifacts. This allowed us to generate a wiring diagram showing functional connections between photoreceptors and ganglion cells. We present a theoretical model that explains the observed intrinsic optical signals by osmotic volume changes, induced by ion influx or efflux. Since all neuronal activity is associated with ion fluxes, imaging osmotic induced size changes with nanometer precision should visualize activation in any neuron.

physics.bio-ph↗

Non-invasive imaging of Young's modulus and Poisson's ratio in cancers in vivo

Objective: Alterations of Young's modulus (YM) and Poisson's ratio (PR) in biological tissues are often early indicators of the onset of pathological conditions. Knowledge of these parameters has been proven to be of great clinical significance for the diagnosis, prognosis and treatment of cancers. Currently, however, there are no non-invasive modalities that can be used to image and quantify these parameters in vivo without assuming incompressibility of the tissue, an assumption that is rarely justified in human tissues. Methods: In this paper, we develop a new method to simultaneously reconstruct YM and PR of a tumor and of its surrounding tissues, irrespective of the boundary conditions and the shape of the tumor based on ellipsoidal approximation. This new non-invasive method allows the generation of high spatial resolution YM and PR maps from axial and lateral strain data obtained via ultrasound elastography. The method was validated using finite element (FE) simulations and controlled experiments performed on phantoms with known mechanical properties. The clinical feasibility of the developed method was also demonstrated in an orthotopic mouse model of breast cancer. Results: Our results from simulations and controlled experiments demonstrate that the proposed reconstruction technique is accurate and robust. Conclusion: Availability of the proposed technique could address the clinical need of a non-invasive modality capable of imaging, quantifying and monitoring the mechanical properties of tumors with high spatial resolution and in real time. Significance: This technique can have a significant impact on the clinical translation of elasticity imaging methods.

eess.IV↗

A Magnetically-Triggered Soft Capsule for On-Demand Mucus Collection

In this work, we present a soft capsule for mucus collection in human intestine for diagnostic purpose, with reduced risk of tissue damage compared with other biopsy methods. The capsule implements passive locomotion and the sampling process is triggered by magnetic field using a permanent magnet, which is placed on the skin above the region of interest (ROI). The capsule contains a soft vacuum chamber which is sealed with wax. When magnetic field and mucus are present simultaneously, the circuit inside the capsule will be closed and nichrome wire will start to generate heat to melt the wax, and mucus will be collected into the vacuum chamber due to air pressure. Experiments on heating capability of nichrome wire, mucus collection and reliability of the capsule are conducted to validate this design.

physics.med-ph↗

Ultrahigh field MR-imaging: new frontiers and possibilities

Increasing the static magnetic field strength into the realm of ultrahigh fields (7 T and higher) is the central trend in modern magnetic resonance (MR) imaging. The use of ultrahigh fields in MR-imaging leads to numerous effects some of them raising the image quality, some degrading, some previously undetected in lower fields. This review aims to outline the main consequences of introducing ultrahigh fields in MR-imaging, including new challenges and the proposed solutions, as well as new scanning possibilities unattainable at lower field strengths (below 7 T).

physics.med-ph↗

Non-invasive assessment of the spatial and temporal distributions of interstitial fluid pressure, fluid velocity and fluid flow in cancers in vivo

Interstitial fluid pressure (IFP), interstitial fluid velocity (IFV), interstitial permeability (IP) and vascular permeability (VP) are cancer mechanopathological parameters of great clinical significance. To date, there is a lack of non-invasive techniques that can be used to estimate these parameters in vivo. In this study, we designed and tested new ultrasound poroelastography methods capable of estimating the magnitude and spatial distribution of fluid pressure, fluid velocity and fluid flow inside tumors. We theoretically proved that fluid pressure, velocity and flow estimated using poroelastography from a tumor under creep compression are directly related to the underlying IFP, IFV and fluid flow, respectively, differing only in peak values. We also proved that, from the spatial distribution of the fluid pressure estimated using poroelastography, it is possible to derive: the parameter alpha, which quantifies the spatial distribution of the IFP; the ratio between VP and IP and the ratio between the peak IFP and effective vascular pressure in the tumor. Finally, we demonstrated that axial strain time constant (TC) elastograms are directly related to VP and IP in tumors. Our techniques were validated using finite element and ultrasound simulations, while experiments on a human breast cancer animal model were used to show the feasibility of these methods in vivo.

eess.IV↗

Clinically Deployed Distributed Magnetic Resonance Imaging Reconstruction: Application to Pediatric Knee Imaging

Magnetic resonance imaging is capable of producing volumetric images without ionizing radiation. Nonetheless, long acquisitions lead to prohibitively long exams. Compressed sensing (CS) can enable faster scanning via sub-sampling with reduced artifacts. However, CS requires significantly higher reconstruction computation, limiting current clinical applications to 2D/3D or limited-resolution dynamic imaging. Here we analyze the practical limitations to T2 Shuffling, a four-dimensional CS-based acquisition, which provides sharp 3D-isotropic-resolution and multi-contrast images in a single scan. Our improvements to the pipeline on a single machine provide a 3x overall reconstruction speedup, which allowed us to add algorithmic changes improving image quality. Using four machines, we achieved additional 2.1x improvement through distributed parallelization. Our solution reduced the reconstruction time in the hospital to 90 seconds on a 4-node cluster, enabling its use clinically. To understand the implications of scaling this application, we simulated running our reconstructions with a multiple scanner setup typical in hospitals.

physics.med-ph↗

Effect of an advanced model-based iterative reconstruction algorithm on texture and visual impression of images privieded by a dual source CT scanner

Purpose: To evaluate the influence of ADMIRE algorithm on image texture and image visual impression as a supplement to measurements of common image quality parameters such as noise levels and spatial resolution. Methods: An ACR phantom was examined at different radiation dose levels. To characterize the image texture, two Haralick texture parameters, contrast and entropy, for different dose level and reconstruction algorithms were assessed. The visual impression of images and their structural differences were evaluated using the structural similarity index (SSIM). Noise was determined for all dose and AMIRE levels and compared to those by filtered back projection (FBP). The spatial resolution was determined by the modulation transfer functions and the line spread function. Results: The Haralick texture parameters decreased with increasing ADMIRE levels I up to V. ADMIRE III, IV and V offered a comparable contrast and entropy to those calculated by FBP with a radiation dose reduction up to 50%. SSIM improved with increasing ADMIRE levels. SSIM calculated by ADMIRE IV and V showed similar values by the filter back projection with a dose decrease up to 50%. Spatial resolution was retained up to 90% dose reduction. With increasing ADMIRE as well as dose level the noise distribution shifted to a more narrow distribution, which was in accordance with the reconstructed images using ADMIRE. Conclusion: Texture analysis and SSIM allow a more realistic assessment of the dose reduction potential of iterative reconstruction algorithms than quality metrics only based on physical measurements of noise distribution or spatial resolution. This work presented that by means of the ADMIRE algorithm, a comparable image quality at reduced radiation doses can be reached.

physics.med-ph↗