3D medical volume segmentation using hybrid multiresolution statistical approaches

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2010 S AlZu’bi and A Amira.3D volume segmentation is the process of partitioning voxels into 3D regions (subvolumes) that represent meaningful physical entities which are more meaningful and easier to analyze and usable in future applications. Multiresolution Analysis (MRA) enables the preservation of an image according to certain levels of resolution or blurring. Because of multiresolution quality, wavelets have been deployed in image compression, denoising, and classification. This paper focuses on the implementation of efficient medical volume segmentation techniques. Multiresolution analysis including 3D wavelet and ridgelet has been used for feature extraction which can be modeled using Hidden Markov Models (HMMs) to segment the volume slices. A comparison study has been carried out to evaluate 2D and 3D techniques which reveals that 3D methodologies can accurately detect the Region Of Interest (ROI). Automatic segmentation has been achieved using HMMs where the ROI is detected accurately but suffers a long computation time for its calculations

Diagnostic Compression of Biomedical Volumes

In this work we deal with lossy compression of biomedical volumes. By force of circumstances, diagnostic compression is bound to a subjective judgment. However, with respect to the algorithms, there is a need to shape the coding methodology so as to highlight beyond compression three important factors: the medical data, the specic usage and the particular end-user. Biomedical volumes may have very dierent characteristics which derive from imaging modality, resolution and voxel aspect ratio. Moreover, volumes are usually viewed slice by slice on a lightbox, according to dierent cutting direction (typically one of the three voxel axes). We will see why and how these aspects impact on the choice of the coding algorithm and on a possible extension of 2D well known algorithms to more ecient 3D versions. Cross-correlation between reconstruction error and signal is a key aspect to keep into account; we suggest to apply a non uniform quantization to wavelet coefficients in order to reduce slice PSNR variation. Once a good neutral coding for a certain volume is obtained, non uniform quantization can also be made space variant in order to reach more objective quality on Volumes of Diagnostic Interest (VoDI), which in turns can determine the diagnostic quality of the entire data set

Framework for 4D medical data compression

U ovom radu predložen je novi programski okvir za kompresiju četvero-dimenzionalnih (4D) medicinskih podataka. Arhitektura ovog programskog okvira temelji se na različitim procedurama i algoritmima koji detektiraju vremenske i prostorne zalihosti u ulaznim 4D medicinskim podacima. Pokret kroz vrijeme analizira se pomoću vektora pomaka koji predstavljaju ulazne parametre za neuronske mreže koje se koriste za procjenu pokreta. Kombinacijom segmentacije, pronalaženja odgovarajućih blokova i predikcijom vektora pomaka, zajedno s ekspertnim znanjem moguće je optimirati performanse sustava. Frekvencijska svojstva se analiziraju proširenjem wavelet transformacije na tri dimenzije. Za mirne volumetrijske objekte, moguće je konstruirati različite wavelet pakete s različitim filtrima koji omogućavaju širok raspon analiza frekvencijskih zalihosti. Kombinacijom uklanjanja vremenskih i prostornih zalihosti moguće je postići vrlo visoke omjere kompresije.This work presents a novel framework for four-dimensional (4D) medical data compression architecture. This framework is based on different procedures and algorithms that detect time and spatial (frequency) redundancy in recorded 4D medical data. Motion in time is analyzed through the motion fields that produce input parameters for the neural network used for motion estimation. Combination of segmentation, block matching and motion field prediction along with expert knowledge are incorporated to achieve better performance. Frequency analysis is done through an extension of one dimensional wavelet transformation to three dimensions. For still volume objects different wavelet packets with different filter banks can be constructed, providing a wide range of frequency analysis. With combination of removing temporal and spatial redundancies, very high compression ratio is achieved

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

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