Automated methods for tuberculosis detection/diagnosis : a literature review

Funding: Welcome Trust Institutional Strategic Support fund of the University of St Andrews, grant code 204821/Z/16/Z.Tuberculosis (TB) is one of the leading infectious causes of death worldwide. The effective management and public health control of this disease depends on early detection and careful treatment monitoring. For many years, the microscopy-based analysis of sputum smears has been the most common method to detect and quantify Mycobacterium tuberculosis (Mtb) bacteria. Nonetheless, this form of analysis is a challenging procedure since sputum examination can only be reliably performed by trained personnel with rigorous quality control systems in place. Additionally, it is affected by subjective judgement. Furthermore, although fluorescence-based sample staining methods have made the procedure easier in recent years, the microscopic examination of sputum is a time-consuming operation. Over the past two decades, attempts have been made to automate this practice. Most approaches have focused on establishing an automated method of diagnosis, while others have centred on measuring the bacterial load or detecting and localising Mtb cells for further research on the phenotypic characteristics of their morphology. The literature has incorporated machine learning (ML) and computer vision approaches as part of the methodology to achieve these goals. In this review, we first gathered publicly available TB sputum smear microscopy image sets and analysed the disparities in these datasets. Thereafter, we analysed the most common evaluation metrics used to assess the efficacy of each method in its particular field. Finally, we generated comprehensive summaries of prior work on ML and deep learning (DL) methods for automated TB detection, including a review of their limitations.Publisher PDFPeer reviewe

An algorithm for detection of tuberculosis bacilli in Ziehl-Neelsen sputum smear images

This work proposes an algorithm oriented to the detection of tuberculosis bacilli in digital images of sputum samples, inked with the Ziehl Neelsen method and prepared with the direct, pellet and diluted pellet methods. The algorithm aims at automating the optical analysis of bacilli count and the calculation of the concentration level. Several algorithms have been proposed in the literature with the same objective, however, in no case is the performance in sensitivity and specificity evaluated for the 3 preparation methods. The proposed algorithm improves the contrast of the colors of interest, then thresholds the image and segments by labeling the objects of interest (bacilli). Each object then has its geometrical descriptors and photometric descriptors. With all this, a characteristic vector is formed, which are used in the training and classification process of an SVM. For the training 225 images obtained by the 3 preparation methods were used. The proposed algorithm reached, for the direct method, a sensitivity level of 93.67% and a specificity level of 89.23%. In the case of the Pellet method, a sensitivity of 92.13% and a specificity of 82.58% was obtained, while for diluted Pellet the sensitivity was 92.81% and the specificity 83.61%

Analysis of Tuberculosis using Smear Image

An automatic method for the detection of Tuberculosis (TB) bacilli from microscopic sputum smear images is presented in this paper. According to WHO, TB is the ninth leading cause of death all over the world. There are various techniques to diagnose TB, of which conventional microscopic sputum smear examination is considered. However, the mentioned method of diagnosis is time intensive and error prone, even in experienced hands. The proposed method performs detection of TB, by image binarization and subsequent classification of detected regions using a convolutional neural network. We have evaluated our gist algorithm using a dataset of sputum smear microscopic images with different backgrounds (high density and low-density images). Experimental results show that the proposed algorithm achieves for the TB detection. The proposed method automatically detects whether the sputum smear images is infected with TB or not. This method will aid clinicians to predict the disease accurately in a short span of time, thereby helping in improving the clinical outcome

Hardware and software integration and testing for the automation of bright-field microscopy for tuberculosis detection

Automated microscopy for the detection of tuberculosis (TB) in sputum smears would reduce the load on technicians, especially in countries with a high TB burden. This dissertation reports on the development and testing of an automated system built around a conventional microscope for the detection of TB in Ziehl-Neelsen (ZN) stained sputum smears. Microscope auto-focusing, image analysis and stage movement were integrated. Images were captured at 40x magnification

Image segmentation and object classification for automatic detection of tuberculosis in sputum smears

Includes bibliographical references (leaves 95-101).An automated microscope is being developed in the MRC/UCT Medical Imaging Research Unit at the University of Cape Town in an effort to ease the workload of laboratory technicians screening sputum smears for tuberculosis (TB), in order to improve screening in countries with a heavy burden of TB. As a step in the development of such a microscope, the project described here was concerned with the extraction and identification of TB bacilli in digital images of sputum smears obtained with a microscope. The investigations were carried out on Ziehl-Neelsen (ZN) stained sputum smears. Different image segmentation methods were compared and object classification was implemented using various two-class classifiers, for images obtained using a microscope with 100x objective lens magnification. The bacillus identification route established for the 100x images, was applied to images obtained using a microscope with 20x objective lens magnification. In addition, one-class classification was applied the 100x images. A combination of pixel classifiers performed best in image segmentation to extract objects of interest. For 100x images, the product of the Bayes’, quadratic and logistic linear classifiers resulted in a percentage of correctly classified bacillus pixels of 89.38%; 39.52% of pixels were incorrectly classified. The segmentation method did not miss any bacillus objects with their length in the focal plane of an image. The biggest source of error for the segmentation method was staining inconsistencies. The pixel segmentation method performed poorly on images with 20x magnification. Geometric change invariant features were extracted to describe segmented objects; Fourier coefficients, moment invariant features and colour features were used. All two-class object classifiers had balanced performance for 100x images, with sensitivity and specificity above 95% for the detection of an individual bacillus after Fisher mapping of the feature set. Object classification on images with 20x magnification performed similarly. One-class object classification using the mixture of Gaussians classifier, without Fisher mapping of features, produced sensitivity and specificity above 90% when applied to 100x images

Towards fully automated analysis of sputum smear microscopy images

Sputum smear microscopy is used for diagnosis and treatment monitoring of pulmonary tuberculosis (TB). Automation of image analysis can make this technique less laborious and more consistent. This research employs artificial intelligence to improve automation of Mycobacterium tuberculosis (Mtb) cell detection, bacterial load quantification, and phenotyping from fluorescence microscopy images. I first introduce a non-learning, computer vision (CV) approach for bacteria detection, employing ridge-based approach using the Hessian matrix to detect ridges of Mtb bacteria, complemented by geometric analysis. The effectiveness of this approach is assessed through a custom metric using the Hu moment vector. Results demonstrate lower performance relative to literature metrics, motivating the need for deep learning (DL) to capture bacterial morphology. Subsequently, I develop an automated pipeline for detection, classification, and counting of bacteria using DL techniques. Firstly, Cycle-GANs transfer labels from labelled to unlabeled fields of view (FOVs). Pre-trained DL models are used for subsequent classification and regression tasks. An ablation study confirms pipeline efficacy, with a count error within 5%. For downstream analysis, microscopy slides are divided into tiles, each of which is sequentially cropped and magnified. A subsequent filtering stage eliminates non-salient FOVs by applying pre-trained DL models along with a novel method that employs dual convolutional neural network (CNN)-based encoders for feature extraction: one encoder is dedicated to learning bacterial appearance, and the other focuses on bacterial shape, which both precede into a bottleneck of a smaller CNN classifier network. The proposed model outperforms others in accuracy, yields no false positives, and excels across decision thresholds. Mtb cell lipid content and length may be related to antibiotic tolerance, underscoring the need to locate bacteria within paired FOV images stained with distinct cell identification and lipid detection, and to measure bacterial dimensions. I employ a proposed UNet-like model for precise bacterial localization. By combining CNNs and feature descriptors, my method automates reporting of both lipid content and cell length. Application of the approaches described here may assist clinical TB care and therapeutics research

A Enhanced Approach for Identification of Tuberculosis for Chest X-Ray Image using Machine Learning

Lungs are the primary organs affected by the infectious illness tuberculosis (TB). Mycobacterium tuberculosis, often known as Mtb, is the bacterium that causes tuberculosis. When a person speaks, spits, coughs, or breathes in, active tuberculosis can quickly spread through the air. Early TB diagnosis takes some time. Early detection of the bacilli allows for straightforward therapy. Chest X-ray images, sputum images, computer-assisted identification, feature selection, neural networks, and active contour technologies are used to diagnose human tuberculosis. Even when several approaches are used in conjunction, a more accurate early TB diagnosis can still be made. Worldwide, this leads to a large number of fatalities. An efficient technology known as the Deep Learning approach is used to diagnose tuberculosis microorganisms. Because this technology outperforms the present methods for early TB diagnosis, Despite the fact that death cannot be prevented, it is possible to lessen its effects

Tuberculosis bacteria detection and counting in fluorescence microscopy images using a multi-stage deep learning pipeline

The manual observation of sputum smears by fluorescence microscopy for the diagnosis and treatment monitoring of patients with tuberculosis (TB) is a laborious and subjective task. In this work, we introduce an automatic pipeline which employs a novel deep learning-based approach to rapidly detect Mycobacterium tuberculosis (Mtb) organisms in sputum samples and thus quantify the burden of the disease. Fluorescence microscopy images are used as input in a series of networks, which ultimately produces a final count of present bacteria more quickly and consistently than manual analysis by healthcare workers. The pipeline consists of four stages: annotation by cycle-consistent generative adversarial networks (GANs), extraction of salient image patches, classification of the extracted patches, and finally, regression to yield the final bacteria count. We empirically evaluate the individual stages of the pipeline as well as perform a unified evaluation on previously unseen data that were given ground-truth labels by an experienced microscopist. We show that with no human intervention, the pipeline can provide the bacterial count for a sample of images with an error of less than 5%.Publisher PDFPeer reviewe

Segmentation of candidate bacillus objects in images of Ziehl-Neelsen-stained sputum smears using deformable models

Includes abstract.Includes bibliographical references (leaves 83-88).Automated microscopy for the detection of tuberculosis (TB) in sputum smears seeks to address the strain on technicians and to achieve faster diagnosis in order to cope with the rising number of TB cases. Image processing techniques provide a useful alternative to the conventional, manual analysis of sputum smears for diagnosis. In the project described here, the use of parametric and geometric deformable models was explored for segmentation of TB bacilli in images of Ziehl-Neelsen-stained sputum smears for automated TB diagnosis. The goal of segmentation is to produce candidate bacillus objects for input into a classifier