Deep learning assisted MRI guided attenuation correction in PET

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological and functional details of the tissue at the molecular level. However, the acquired PET images have some limitations such as the attenuation. PET attenuation correction is an essential step to obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners, magnetic resonance (MR) images are used to address the problem of PET attenuation correction. The MR images segmentation is one simple and robust approach to create pseudo computed tomography (CT) images, which are used to generate attenuation coefficient maps to correct the PET attenuation. Recently, deep learning has been proposed and used as a promising technique to efficiently perform MR and various medical images segmentation. In this research work, deep learning guided segmentation approaches have been proposed to enhance the bone class segmentation of MR brain images in order to generate accurate pseudo-CT images. The first approach has introduced the combination of handcrafted features with deep learning features to enrich the set of features. Multiresolution analysis techniques, which generate multiscale and multidirectional coefficients of an image such as contourlet and shearlet transforms, are applied and combined with deep convolutional neural network (CNN) features. Different experiments have been conducted to investigate the number of selected coefficients and the insertion location of the handcrafted features. The second approach aims at reducing the segmentation algorithm’s complexity while maintaining the segmentation performance. An attention based convolutional encode-decoder network has been proposed to adaptively recalibrate the deep network features. This attention based network consists of two different squeeze and excitation blocks that excite the features spatially and channel wise. The two blocks are combined sequentially to decrease the number of network’s parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w images. Multiple fine tuning approaches and experiments have been conducted to study the best fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been used to carry an objective evaluation to measure the segmentation performance of the results obtained by the three proposed methods. The first and second approaches have been validated with other studies in the literature that applied deep network based segmentation technique to perform MR based attenuation correction for PET images. The proposed methods have shown an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC) from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%. The proposed excitation-based CNN has decreased the model complexity by decreasing the number of trainable parameters by more than 46% where less computing resources are required to train the model. The proposed hybrid transfer learning method has shown its superiority to build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied transfer learning methods especially with the bone class where the DSC is increased from 0.3841 to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than transfer learning using open and conservative fine tuning

A Novel Multi-Focus Image Fusion Method Based on Stochastic Coordinate Coding and Local Density Peaks Clustering

abstract: The multi-focus image fusion method is used in image processing to generate all-focus images that have large depth of field (DOF) based on original multi-focus images. Different approaches have been used in the spatial and transform domain to fuse multi-focus images. As one of the most popular image processing methods, dictionary-learning-based spare representation achieves great performance in multi-focus image fusion. Most of the existing dictionary-learning-based multi-focus image fusion methods directly use the whole source images for dictionary learning. However, it incurs a high error rate and high computation cost in dictionary learning process by using the whole source images. This paper proposes a novel stochastic coordinate coding-based image fusion framework integrated with local density peaks. The proposed multi-focus image fusion method consists of three steps. First, source images are split into small image patches, then the split image patches are classified into a few groups by local density peaks clustering. Next, the grouped image patches are used for sub-dictionary learning by stochastic coordinate coding. The trained sub-dictionaries are combined into a dictionary for sparse representation. Finally, the simultaneous orthogonal matching pursuit (SOMP) algorithm is used to carry out sparse representation. After the three steps, the obtained sparse coefficients are fused following the max L1-norm rule. The fused coefficients are inversely transformed to an image by using the learned dictionary. The results and analyses of comparison experiments demonstrate that fused images of the proposed method have higher qualities than existing state-of-the-art methods

Structural similarity loss for learning to fuse multi-focus images

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Convolutional neural networks have recently been used for multi-focus image fusion. However, some existing methods have resorted to adding Gaussian blur to focused images, to simulate defocus, thereby generating data (with ground-truth) for supervised learning. Moreover, they classify pixels as ‘focused’ or ‘defocused’, and use the classified results to construct the fusion weight maps. This then necessitates a series of post-processing steps. In this paper, we present an end-to-end learning approach for directly predicting the fully focused output image from multi-focus input image pairs. The suggested approach uses a CNN architecture trained to perform fusion, without the need for ground truth fused images. The CNN exploits the image structural similarity (SSIM) to calculate the loss, a metric that is widely accepted for fused image quality evaluation. What is more, we also use the standard deviation of a local window of the image to automatically estimate the importance of the source images in the final fused image when designing the loss function. Our network can accept images of variable sizes and hence, we are able to utilize real benchmark datasets, instead of simulated ones, to train our network. The model is a feed-forward, fully convolutional neural network that can process images of variable sizes during test time. Extensive evaluation on benchmark datasets show that our method outperforms, or is comparable with, existing state-of-the-art techniques on both objective and subjective benchmarks

Image Simulation in Remote Sensing

Remote sensing is being actively researched in the fields of environment, military and urban planning through technologies such as monitoring of natural climate phenomena on the earth, land cover classification, and object detection. Recently, satellites equipped with observation cameras of various resolutions were launched, and remote sensing images are acquired by various observation methods including cluster satellites. However, the atmospheric and environmental conditions present in the observed scene degrade the quality of images or interrupt the capture of the Earth's surface information. One method to overcome this is by generating synthetic images through image simulation. Synthetic images can be generated by using statistical or knowledge-based models or by using spectral and optic-based models to create a simulated image in place of the unobtained image at a required time. Various proposed methodologies will provide economical utility in the generation of image learning materials and time series data through image simulation. The 6 published articles cover various topics and applications central to Remote sensing image simulation. Although submission to this Special Issue is now closed, the need for further in-depth research and development related to image simulation of High-spatial and spectral resolution, sensor fusion and colorization remains.I would like to take this opportunity to express my most profound appreciation to the MDPI Book staff, the editorial team of Applied Sciences journal, especially Ms. Nimo Lang, the assistant editor of this Special Issue, talented authors, and professional reviewers