In computed tomographic imaging, model based iterative reconstruction methods have generally shown better image quality than the more traditional, faster filtered backprojection technique. The cost we have to pay is that MBIR is computationally expensive. In this work we train a 2.5D deep learning (DL) network to mimic MBIR quality image. The network is realized by a modified Unet, and trained using clinical FBP and MBIR image pairs. We achieve the quality of MBIR images faster and with a much smaller computation cost. Visually and in terms of noise power spectrum (NPS), DL-MBIR images have texture similar to that of MBIR, with reduced noise power. Image profile plots, NPS plots, standard deviation, etc. suggest that the DL-MBIR images result from a successful emulation of an MBIR operator.

In this work, we perform direct material reconstruction from spectral CT data using a model based iterative reconstruction (MBIR) approach. Material concentrations are measured in volume fractions, whose total is constrained by a maximum of unity. A phantom containing a combination of 4 basis materials (water, iodine, gadolinium, calcium) was scanned using a photon-counting detector. Iodine and gadolinium were chosen because of their common use as contrast agents in CT imaging. Scan data was binned into 5 energy (keV) levels. Each energy bin in a calibration scan was reconstructed, allowing the linear attenuation coefficient of each material for every energy to be estimated by a least-squares fit to ground truth in the image domain. The resulting $5\times 4$ matrix, for $5$ energies and $4$ materials, is incorporated into the forward model in direct reconstruction of the $4$ basis material images with spatial and/or inter-material regularization. In reconstruction from a subsequent low-concentration scan, volume fractions within regions of interest (ROIs) are found to be close to the ground truth. This work is meant to lay the foundation for further work with phantoms including spatially coincident mixtures of contrast materials and/or contrast agents in widely varying concentrations, molecular imaging from animal scans, and eventually clinical applications.

Deep learning (DL) shows promise of advantages over conventional signal processing techniques in a variety of imaging applications. The networks’ being trained from examples of data rather than explicitly designed allows them to learn signal and noise characteristics to most effectively construct a mapping from corrupted data to higher quality representations. In inverse problems, one has options of applying DL in the domain of the originally captured data, in the transformed domain of the desired final representation, or both. X-ray computed tomography (CT), one of the most valuable tools in medical diagnostics, is already being improved by DL methods. Whether for removal of common quantum noise resulting from the Poisson-distributed photon counts, or for reduction of the ill effects of metal implants on image quality, researchers have begun employing DL widely in CT. The selection of training data is driven quite directly by the corruption on which the focus lies. However, the way in which differences between the target signal and measured data is penalized in training generally follows conventional, pointwise loss functions. This work introduces a creative technique for favoring reconstruction characteristics that are not well described by norms such as mean-squared or mean-absolute error. Particularly in a field such as X-ray CT, where radiologists’ subjective preferences in image characteristics are key to acceptance, it may be desirable to penalize differences in DL more creatively. This penalty may be applied in the data domain, here the CT sinogram, or in the reconstructed image. We design loss functions for both shaping and selectively preserving frequency content of the signal.

There is growing interest in employing deep neural networks (DNN) for image sharpening. However, sharpening medical computed tomography (CT) images is challenging because sharpening substantially amplifies high-frequency noise. Alternatively, sharpening algorithms that are also designed to denoise produce images lacking texture. Most importantly, radiologists strongly prefer reading images at a consistent level of noise. Hence it is preferable that a sharpening algorithm not substantially change the noise energy or texture. In this work, we propose a noise preserving sharpening filter (NPSF) to sharpen CT images while keeping the noise energy and texture in the result similar to that of the input. We achieve this by adding appropriately scaled noise while training. Furthermore, the NPSF is characterized by three user-adjustable parameters which give flexibility to achieve a desired level of sharpness and noise. Our experiments show that the NPSF can sharpen noisy images while producing desired noise level and texture.

Low x-ray dose is desirable in x-ray computed tomographic (CT) imaging due to health concerns. But low dose comes with a cost of low signal artifacts such as streaks and low frequency bias in the reconstruction. As a result, low signal correction is needed to help reduce artifacts while retaining relevant anatomical structures. Low signal can be encountered in cases where sufficient number of photons do not reach the detector to have confidence in the recorded data. X-ray photons, assumed to have Poisson distribution, have signal to noise ratio proportional to the dose, with poorer SNR in low signal areas. Electronic noise added by the data acquisition system further reduces the signal quality. In this paper we will demonstrate a technique to combat low signal artifacts through adaptive filtration. It entails statistics-based filtering on the uncorrected data, correcting the lower signal areas more aggressively than the high signal ones. We look at local averages to decide how aggressive the filtering should be, and local standard deviation to decide how much detail preservation to apply. Implementation consists of a pre-correction step i.e. local linear minimum mean-squared error correction, followed by a variance stabilizing transform, and finally adaptive bilateral filtering. The coefficients of the bilateral filter are computed using local statistics. Results show that improvements were made in terms of low frequency bias, streaks, local average and standard deviation, modulation transfer function and noise power spectrum.

There is growing interest in the use of deep neural network (DNN) based image denoising to reduce patient’s X-ray dosage in medical computed tomography (CT). An effective denoiser must remove noise while maintaining the texture and detail. Commonly used mean squared error (MSE) loss functions in the DNN training weight errors due to bias and variance equally. However, the error due to bias is often more egregious since it results in loss of image texture and detail. In this paper, we present a novel approach to designing a loss function that penalizes variance and bias differently. Our proposed bias-reducing loss function allows us to train a DNN denoiser so that the amount of texture and detail retained can be controlled through a user adjustable parameter. Our experiments verify that the proposed loss function enhances the texture and detail in denoised images with only a slight increase in the MSE.

Biomedical imaging is a series of procedures which create images of the human body, or parts of the body, to help screen for possible illness or injury, diagnose the likely cause of symptoms and monitor health conditions or the effects of treatment. The objective of the paper is to provide an overview about various bio medical imaging techniques used in detection and diagnosis of Cancer. Each of these imaging techniques provides information about the anatomy, chemical or physiologic phenomena of the human body which are studied independently by doctors to identify Cancer. The biomedical imaging systems, applications, benefits, drawbacks and research challenges are discussed. Image Fusion and its role in Bio medical imaging is also discussed. Image Fusion is the process of fusing two or more bio medical images which contain complementary information into a single composite image. These enrich image quality and avoid redundancy thereby increase the clinical applicability of medical images for cancer detection, prognosis and treatment planning of Cancer.

Model-Based Iterative Reconstruction (MBIR) has shown promising results in clinical studies as they allow significant dose reduction during CT scans while maintaining the diagnostic image quality. MBIR improves the image quality over analytical reconstruction by modeling both the sensor (e.g., forward model) and the image being reconstructed (e.g., prior model). While the forward model is typically based on the physics of the sensor, accurate prior modeling remains a challenging problem. Markov Random Field (MRF) has been widely used as prior models in MBIR due to simple structure, but they cannot completely capture the subtle characteristics of complex images. To tackle this challenge, we generate a prior model by learning the desirable image property from a large dataset. Toward this, we use Plug-and-Play (PnP) framework which decouples the forward model and the prior model in the optimization procedure, replacing the prior model optimization by a image denoising operator. Then, we adopt the state-of-the-art deep residual learning for the image denoising operator which represents the prior model in MBIR. Experimental results on real CT scans demonstrate that our PnP MBIR with deep residual learning prior significantly reduces the noise and artifacts compared to analytical reconstruction and standard MBIR with MRF prior.

High-attenuation materials pose significant challenges to computed tomographic imaging. Formed of high mass-density and high atomic number elements, they cause more severe beam hardening and scattering artifacts than do water-like materials. Pre-corrected line-integral density measurements are no longer linearly proportional to the path lengths, leading to reconstructed image suffering from streaking artifacts extending from metal, often along highest-density directions. In this paper, a novel prior-based iterative approach is proposed to reduce metal artifacts. It combines the superiority of statistical methods with the benefits of sinogram completion methods to estimate and correct metal-induced biases. Preliminary results show minimized residual artifacts and significantly improved image quality.

While Model Based Iterative Reconstruction (MBIR) of CT scans has been shown to have better image quality than Filtered Back Projection (FBP), its use has been limited by its high computational cost. More recently, deep convolutional neural networks (CNN) have shown great promise in both denoising and reconstruction applications. In this research, we propose a fast reconstruction algorithm, which we call Deep Learning MBIR (DL-MBIR), for approximating MBIR using a deep residual neural network. The DL-MBIR method is trained to produce reconstructions that approximate true MBIR images using a 16 layer residual convolutional neural network implemented on multiple GPUs using Google Tensorflow. In addition, we propose 2D, 2.5D and 3D variations on the DL-MBIR method and show that the 2.5D method achieves similar quality to the fully 3D method, but with reduced computational cost.

With the recent introduction of CT scanners with large cone angles, wide coverage detectors now provide a desirable scanning platform for cardiac CT that allows whole heart imaging in a single rotation. On these scanners, while half-scan data is strictly sufficient to produce images with the best temporal resolution, acquiring a full 360 degree rotation worth of data is beneficial for wide-cone image reconstruction at negligible additional radiation dose. Applying Model-Based Iterative Reconstruction (MBIR) algorithm to the heart has shown to yield significant enhancement in image quality for cardiac CT. But imaging the heart in large cone angle geometry leads to apparently conflicting data usage considerations. On the one hand, in addition to using the fastest available scanner rotation speed, a minimal complete data set of 180 degrees plus the fan angle is typically used to minimize both cardiac and respiratory motion. On the other hand, a full 360 degree acquisition helps better handle the challenges of missing frequencies and incomplete projections associated with wide-cone half-scan data acquisition. In this paper, we develop a Spatially Adaptive sinogram Weights MBIR algorithm (SAW-MBIR) that is designed to achieve the benefits of both half and full-scan reconstructions in order to maximize temporal resolution over the heart region while providing stable results over the whole volume covered with the wide-area detector. Spatially-adaptive sinogram weights applied to each projection measurement in SAW-MBIR are designed to selectively perform backprojection from the full and half-scan portion of the sinogram based on both projection angle and reconstructed voxel location. We demonstrate with experimental results of SAW-MBIR applied to whole-heart cardiac CT clinical data that overall temporal resolution matches half-scan while full volume image quality is on par with full-scan MBIR.

Model based iterative reconstruction (MBIR) algorithms have shown significant improvement in CT image quality by increasing resolution as well as reducing noise and artifacts. In diagnostic protocols, radiologists often need the high-resolution reconstruction of a limited region of interest (ROI). This ROI reconstruction is complicated for MBIR which should reconstruct an image in a full field of view (FOV) given full sinogram measurements. Multi-resolution approaches are widely used for this ROI reconstruction of MBIR, in which the image with a full FOV is reconstructed in a low-resolution and the forward projection of non-ROI is subtracted from the original sinogram measurements for high-resolution ROI reconstruction. However, a low-resolution reconstruction of a full FOV can be susceptible to streaking and blurring artifacts and these can be propagated into the following high-resolution ROI reconstruction. To tackle this challenge, we use a coupled dictionary representation model between low- and high-resolution training dataset for artifact removal and super resolution of a low-resolution full FOV reconstruction. Experimental results on phantom data show that the restored full FOV reconstruction via a coupled dictionary learning significantly improve the image quality of high-resolution ROI reconstruction for MBIR.

X-ray detectors in clinical computed tomography (CT) usually operate in current-integrating mode. Their complicated signal statistics often lead to intractable likelihood functions for practical use in model-based image reconstruction (MBIR). It is therefore desirable to design simplified statistical models without losing the essential factors. Depending on whether the CT transmission data are logarithmically transformed, pre-log and post-log models are two major categories of choices in CT MBIR. Both being approximations, it remains an open question whether one model can notably improve image quality over the other on real scanners. In this study, we develop and compare several pre-log and post-log MBIR algorithms under a unified framework. Their reconstruction accuracy based on simulation and clinical datasets are evaluated. The results show that pre-log MBIR can achieve notably better quantitative accuracy than post-log MBIR in ultra-low-dose CT, although in less extreme cases, post-log MBIR with handcrafted pre-processing remains a competitive alternative. Pre-log MBIR could play a growing role in emerging ultra-low-dose CT applications.

An increasing number of X-ray CT procedures are being conducted with drastically reduced dosage, due at least in part to advances in statistical reconstruction methods that can deal more effectively with noise than can traditional techniques. As data become photon-limited, more detailed models are necessary to deal with count rates that drop to the levels of system electronic noise. We present two options for sinogram pre-treatment that can improve the performance of photon-starved measurements, with the intent of following with model-based image reconstruction. Both the local linear minimum mean-squared error (LLMMSE) filter and pointwise Bayesian restoration (PBR) show promise in extracting useful, quantitative information from very low-count data by reducing local bias while maintaining the lower noise variance of statistical methods. Results from clinical data demonstrate the potential of both techniques.

Markov random fields (MRFs) have been widely used as prior models in various inverse problems such as tomographic reconstruction. While MRFs provide a simple and often effective way to model the spatial dependencies in images, they suffer from the fact that parameter estimation is difficult. In practice, this means that MRFs typically have very simple structure that cannot completely capture the subtle characteristics of complex images. In this paper, we present a novel Gaussian mixture Markov random field model (GM-MRF) that can be used as a very expressive prior model for inverse problems such as denoising and reconstruction. The GM-MRF forms a global image model by merging together individual Gaussian-mixture models (GMMs) for image patches. In addition, we present a novel analytical framework for computing MAP estimates using the GM-MRF prior model through the construction of surrogate functions that result in a sequence of quadratic optimizations. We also introduce a simple but effective method to adjust the GM-MRF so as to control the sharpness in low- and high-contrast regions of the reconstruction separately. We demonstrate the value of the model with experiments including image denoising and low-dose CT reconstruction.

Beam hardening is a well-known effect in X-ray CT scanning that is caused by the interaction of a broad polychromatic source spectrum with energy-dependent material attenuation. If the scanned object only consists of a single material, the beam hardening effect can be corrected by sinogram precorrection techniques. However, when multiple materials are present, it becomes much more difficult to fully compensate for this distortion; in general, the beam hardening can contribute to reconstruction artifacts such as cupping and streaking. In this paper, we present a novel model-based iterative reconstruction algorithm that incorporates beam hardening correction (MBIR-BHC). Unlike most correction algorithms, which require knowledge of the X-ray spectrum or mass attenuation functions, the MBIR-BHC algorithm works by simultaneously reconstructing the image and estimating the beam-hardening function. The method is based on the assumption that the object is formed by a combination of two distinct materials that can be separated based on their densities. We formulate a poly-energetic X-ray forward model using a polynomial function of two material projections: one for the low density material and one for the high. We then develop an alternating minimization algorithm for jointly estimating the reconstructed image, the material segmentation, and the coefficients of the two component polynomial that models the beam-hardening function. With this approach, the spectrum and mass attenuation functions are not needed in advance, and the correction is adapted to the dataset being reconstructed. We examine the performance of the proposed algorithm using both simulated and real datasets. Results indicate that the MBIR-BHC algorithm significantly reduces several reconstruction artifacts without advanced knowledge of the X-ray spectrum and material properties.