Interactive volumetric segmentation for textile micro-tomography data using wavelets and nonlocal means

This work addresses segmentation of volumetric images of woven carbon fiber textiles from micro-tomography data. We propose a semi-supervised algorithm to classify carbon fibers that requires sparse input as opposed to completely labeled images. The main contributions are: (a) design of effective discriminative classifiers, for three-dimensional textile samples, trained on wavelet features for segmentation; (b) coupling of previous step with nonlocal means as simple, efficient alternative to the Potts model; and (c) demonstration of reuse of classifier to diverse samples containing similar content. We evaluate our work by curating test sets of voxels in the absence of a complete ground truth mask. The algorithm obtains an average 0.95 F1 score on test sets and average F1 score of 0.93 on new samples. We conclude with discussion of failure cases and propose future directions toward analysis of spatiotemporal high-resolution micro-tomography images

3D Medical Image Lossless Compressor Using Deep Learning Approaches

The ever-increasing importance of accelerated information processing, communica-tion, and storing are major requirements within the big-data era revolution. With the extensive rise in data availability, handy information acquisition, and growing data rate, a critical challenge emerges in efficient handling. Even with advanced technical hardware developments and multiple Graphics Processing Units (GPUs) availability, this demand is still highly promoted to utilise these technologies effectively. Health-care systems are one of the domains yielding explosive data growth. Especially when considering their modern scanners abilities, which annually produce higher-resolution and more densely sampled medical images, with increasing requirements for massive storage capacity. The bottleneck in data transmission and storage would essentially be handled with an effective compression method. Since medical information is critical and imposes an influential role in diagnosis accuracy, it is strongly encouraged to guarantee exact reconstruction with no loss in quality, which is the main objective of any lossless compression algorithm. Given the revolutionary impact of Deep Learning (DL) methods in solving many tasks while achieving the state of the art results, includ-ing data compression, this opens tremendous opportunities for contributions. While considerable efforts have been made to address lossy performance using learning-based approaches, less attention was paid to address lossless compression. This PhD thesis investigates and proposes novel learning-based approaches for compressing 3D medical images losslessly.Firstly, we formulate the lossless compression task as a supervised sequential prediction problem, whereby a model learns a projection function to predict a target voxel given sequence of samples from its spatially surrounding voxels. Using such 3D local sampling information efficiently exploits spatial similarities and redundancies in a volumetric medical context by utilising such a prediction paradigm. The proposed NN-based data predictor is trained to minimise the differences with the original data values while the residual errors are encoded using arithmetic coding to allow lossless reconstruction.Following this, we explore the effectiveness of Recurrent Neural Networks (RNNs) as a 3D predictor for learning the mapping function from the spatial medical domain (16 bit-depths). We analyse Long Short-Term Memory (LSTM) models’ generalisabil-ity and robustness in capturing the 3D spatial dependencies of a voxel’s neighbourhood while utilising samples taken from various scanning settings. We evaluate our proposed MedZip models in compressing unseen Computerized Tomography (CT) and Magnetic Resonance Imaging (MRI) modalities losslessly, compared to other state-of-the-art lossless compression standards.This work investigates input configurations and sampling schemes for a many-to-one sequence prediction model, specifically for compressing 3D medical images (16 bit-depths) losslessly. The main objective is to determine the optimal practice for enabling the proposed LSTM model to achieve a high compression ratio and fast encoding-decoding performance. A solution for a non-deterministic environments problem was also proposed, allowing models to run in parallel form without much compression performance drop. Compared to well-known lossless codecs, experimental evaluations were carried out on datasets acquired by different hospitals, representing different body segments, and have distinct scanning modalities (i.e. CT and MRI).To conclude, we present a novel data-driven sampling scheme utilising weighted gradient scores for training LSTM prediction-based models. The objective is to determine whether some training samples are significantly more informative than others, specifically in medical domains where samples are available on a scale of billions. The effectiveness of models trained on the presented importance sampling scheme was evaluated compared to alternative strategies such as uniform, Gaussian, and sliced-based sampling

Detail-preserving and Content-aware Variational Multi-view Stereo Reconstruction

Accurate recovery of 3D geometrical surfaces from calibrated 2D multi-view images is a fundamental yet active research area in computer vision. Despite the steady progress in multi-view stereo reconstruction, most existing methods are still limited in recovering fine-scale details and sharp features while suppressing noises, and may fail in reconstructing regions with few textures. To address these limitations, this paper presents a Detail-preserving and Content-aware Variational (DCV) multi-view stereo method, which reconstructs the 3D surface by alternating between reprojection error minimization and mesh denoising. In reprojection error minimization, we propose a novel inter-image similarity measure, which is effective to preserve fine-scale details of the reconstructed surface and builds a connection between guided image filtering and image registration. In mesh denoising, we propose a content-aware $\ell_{p}$-minimization algorithm by adaptively estimating the $p$ value and regularization parameters based on the current input. It is much more promising in suppressing noise while preserving sharp features than conventional isotropic mesh smoothing. Experimental results on benchmark datasets demonstrate that our DCV method is capable of recovering more surface details, and obtains cleaner and more accurate reconstructions than state-of-the-art methods. In particular, our method achieves the best results among all published methods on the Middlebury dino ring and dino sparse ring datasets in terms of both completeness and accuracy.Comment: 14 pages,16 figures. Submitted to IEEE Transaction on image processin

Cancer diagnosis using deep learning: A bibliographic review

In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann’s machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements

Medical image enhancement

Each image acquired from a medical imaging system is often part of a two-dimensional (2-D) image set whose total presents a three-dimensional (3-D) object for diagnosis. Unfortunately, sometimes these images are of poor quality. These distortions cause an inadequate object-of-interest presentation, which can result in inaccurate image analysis. Blurring is considered a serious problem. Therefore, “deblurring” an image to obtain better quality is an important issue in medical image processing. In our research, the image is initially decomposed. Contrast improvement is achieved by modifying the coefficients obtained from the decomposed image. Small coefficient values represent subtle details and are amplified to improve the visibility of the corresponding details. The stronger image density variations make a major contribution to the overall dynamic range, and have large coefficient values. These values can be reduced without much information loss