Automating three-dimensional osteoarthritis histopathological grading of human osteochondral tissue using machine learning on contrast-enhanced micro-computed tomography

Abstract. Osteoarthritis (OA) is a joint disease affecting hundreds of millions of people worldwide. In basic research, accurate ex vivo measures are needed for assessing OA severity. The standard method for this is the histopathological grading of stained thin tissue sections. However, the methods are destructive, time-consuming, do not describe the full sample volume and provide subjective results. Contrast-enhanced micro-computed tomography (CEμCT) -based grading with phosphotungstic acid -stain was previously developed to address some of these issues. Aim of this study was to investigate the possibility of automating this process. Osteochondral tissue cores were harvested from total knee arthroplasty patients (n = 34, N = 19, Ø = 2 mm, n = 15, N = 5, Ø = 4 mm) and asymptomatic cadavers (n = 30, N = 2, Ø = 4 mm). Samples were imaged with CEμCT, reconstructed and graded manually. Subsequently, the reconstructions were loaded into an ad hoc developed Python software, where volumes-of-interest (VOI) were extracted from different cartilage zones: surface zone (SZ), deep zone (DZ) and calcified zone (CZ) and collapsed into two-dimensional texture images. Normalized images underwent Median Robust Extended Local Binary Pattern (MRELBP) -algorithm to extract the features, with subsequent dimensionality reduction. Ridge and logistic regression models were trained with L2 regularization against the ground truth for the small samples (Ø = 2 mm) using leave-one-patient-out cross-validation. Trained models were then evaluated on the large samples (Ø = 4 mm). Performance of the models were assessed using Spearman’s correlation, Area under the Receiver Operating Characteristic Curve (AUC) and Average Precision (AP). Highest performance on both models was for the SZ. Strong correlation was observed on ridge regression (ρ = 0.68, p < 0.0001), as well as high AUC and AP values for the logistic regression (AUC = 0.92, AP = 0.89) for the small samples. Using the large samples, similar findings were observed with slightly reduced values (ρ = 0.55, p = 0.0001, AUC = 0.86, AP = 0.89). Moderate results were observed for CZ and DZ models (ρ = 0.54 and 0.38, AUC = 0.77 and 0.72, AP = 0.71 and 0.50, respectively). Evaluation on the large samples resulted in performance decrease on CZ models (ρ = 0.29, AUC = 0.63, AP = 0.62), while surprisingly performance increased on DZ logistic regression model (ρ = 0.34, AUC = 0.72, AP = 0.83). Obtained results indicate that automating the 3D CEμCT histopathological grading is feasible. However, with low number of samples, models are better suited for binary detection of sample degenerative features, rather than predicting a detailed grade. To facilitate model generalization on new data, similar data acquisition protocol should be used on all samples. The proposed methods have potential to aid OA researchers and pathologists in 3D histopathological grading, introducing more objectivity to the grading process. This thesis presents the conducted study in detail, and provides an extensive review related to the osteochondral unit, CEμCT imaging, as well as statistical learning machines

Statistical Process Control based on Multivariate Image Analysis: A new proposal for monitoring and defect detection

The monitoring, fault detection and visualization of defects are a strategic issue for product quality. This paper presents a novel methodology based on the integration of textural Multivariate image analysis (MIA) and multivariate statistical process control (MSPC) for process monitoring. The proposed approach combines MIA and p-control charts, as well as T2 and RSS images for defect location and visualization. Simulated images of steel plates are used to illustrate the monitoring performance of it. Both approaches are also applied on real clover images.The authors want to thank Ole Mathis Kruse and Prof. Cecilia Futsaether, from the Norwegian University of Life Sciences (Dept. of Mathematic Sciences and Technology), for providing the real image data set. This research work was partially supported by the Spanish Ministry of Economy and Competitiveness under the project DPI 2011-28112-C04-02.Prats Montalbán, JM.; Ferrer Riquelme, AJ. (2014). Statistical Process Control based on Multivariate Image Analysis: A new proposal for monitoring and defect detection. Computers and Chemical Engineering. 71:501-511. https://doi.org/10.1016/j.compchemeng.2014.09.014S5015117

SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system

Background: SpectraClassifier (SC) is a Java solution for designing and implementing Magnetic Resonance Spectroscopy (MRS)-based classifiers. The main goal of SC is to allow users with minimum background knowledge of multivariate statistics to perform a fully automated pattern recognition analysis. SC incorporates feature selection (greedy stepwise approach, either forward or backward), and feature extraction (PCA). Fisher Linear Discriminant Analysis is the method of choice for classification. Classifier evaluation is performed through various methods: display of the confusion matrix of the training and testing datasets; K-fold cross-validation, leave-one-out and bootstrapping as well as Receiver Operating Characteristic (ROC) curves. Results: SC is composed of the following modules: Classifier design, Data exploration, Data visualisation, Classifier evaluation, Reports, and Classifier history. It is able to read low resolution in-vivo MRS (single-voxel and multi-voxel) and high resolution tissue MRS (HRMAS), processed with existing tools (jMRUI, INTERPRET, 3DiCSI or TopSpin). In addition, to facilitate exchanging data between applications, a standard format capable of storing all the information needed for a dataset was developed. Each functionality of SC has been specifically validated with real data with the purpose of bug-testing and methods validation. Data from the INTERPRET project was used. Conclusions: SC is a user-friendly software designed to fulfil the needs of potential users in the MRS community. It accepts all kinds of pre-processed MRS data types and classifies them semi-automatically, allowing spectroscopists to concentrate on interpretation of results with the use of its visualisation tools

An Extended Review on Fabric Defects and Its Detection Techniques

In Textile Industry, Quality of the Fabric is the main important factor. At the initial stage, it is very essential to identify and avoid the fabrics faults/defects and hence human perception consumes lot of time and cost to reveal the fabrics faults. Now-a-days Automated Inspection Systems are very useful to decrease the fault prediction time and gives best visualizing clarity- based on computer vision and image processing techniques. This paper made an extended review about the quality parameters in the fiber-to-fabric process, fabrics defects detection terminologies applied on major three clusters of fabric defects knitting, woven and sewing fabric defects. And this paper also explains about the statistical performance measures which are used to analyze the defect detection process. Also, comparison among the methods proposed in the field of fabric defect detection

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe

A comprehensive review of fruit and vegetable classification techniques

Recent advancements in computer vision have enabled wide-ranging applications in every field of life. One such application area is fresh produce classification, but the classification of fruit and vegetable has proven to be a complex problem and needs to be further developed. Fruit and vegetable classification presents significant challenges due to interclass similarities and irregular intraclass characteristics. Selection of appropriate data acquisition sensors and feature representation approach is also crucial due to the huge diversity of the field. Fruit and vegetable classification methods have been developed for quality assessment and robotic harvesting but the current state-of-the-art has been developed for limited classes and small datasets. The problem is of a multi-dimensional nature and offers significantly hyperdimensional features, which is one of the major challenges with current machine learning approaches. Substantial research has been conducted for the design and analysis of classifiers for hyperdimensional features which require significant computational power to optimise with such features. In recent years numerous machine learning techniques for example, Support Vector Machine (SVM), K-Nearest Neighbour (KNN), Decision Trees, Artificial Neural Networks (ANN) and Convolutional Neural Networks (CNN) have been exploited with many different feature description methods for fruit and vegetable classification in many real-life applications. This paper presents a critical comparison of different state-of-the-art computer vision methods proposed by researchers for classifying fruit and vegetable

Texture and Colour in Image Analysis

Research in colour and texture has experienced major changes in the last few years. This book presents some recent advances in the field, specifically in the theory and applications of colour texture analysis. This volume also features benchmarks, comparative evaluations and reviews

Image texture analysis for inferential sensing in the process industries

Thesis (MScEng)-- Stellenbosch University, 2013.ENGLISH ABSTRACT: The measurement of key process quality variables is important for the efficient and economical operation of many chemical and mineral processing systems, as these variables can be used in process monitoring and control systems to identify and maintain optimal process conditions. However, in many engineering processes the key quality variables cannot be measured directly with standard sensors. Inferential sensing is the real-time prediction of such variables from other, measurable process variables through some form of model. In vision-based inferential sensing, visual process data in the form of images or video frames are used as input variables to the inferential sensor. This is a suitable approach when the desired process quality variable is correlated with the visual appearance of the process. The inferential sensor model is then based on analysis of the image data. Texture feature extraction is an image analysis approach by which the texture or spatial organisation of pixels in an image can be described. Two texture feature extraction methods, namely the use of grey-level co-occurrence matrices (GLCMs) and wavelet analysis, have predominated in applications of texture analysis to engineering processes. While these two baseline methods are still widely considered to be the best available texture analysis methods, several newer and more advanced methods have since been developed, which have properties that should theoretically provide these methods with some advantages over the baseline methods. Specifically, three advanced texture analysis methods have received much attention in recent machine vision literature, but have not yet been applied extensively to process engineering applications: steerable pyramids, textons and local binary patterns (LBPs). The purpose of this study was to compare the use of advanced image texture analysis methods to baseline texture analysis methods for the prediction of key process quality variables in specific process engineering applications. Three case studies, in which texture is thought to play an important role, were considered: (i) the prediction of platinum grade classes from images of platinum flotation froths, (ii) the prediction of fines fraction classes from images of coal particles on a conveyor belt, and (iii) the prediction of mean particle size classes from images of hydrocyclone underflows. Each of the five texture feature sets were used as inputs to two different classifiers (K-nearest neighbours and discriminant analysis) to predict the output variable classes for each of the three case studies mentioned above. The quality of the features extracted with each method was assessed in a structured manner, based their classification performances after the optimisation of the hyperparameters associated with each method. In the platinum froth flotation case study, steerable pyramids and LBPs significantly outperformed the GLCM, wavelet and texton methods. In the case study of coal fines fractions, the GLCM method was significantly outperformed by all four other methods. Finally, in the hydrocyclone underflow case study, steerable pyramids and LBPs significantly outperformed GLCM and wavelet methods, while the result for textons was inconclusive. Considering all of these results together, the overall conclusion was drawn that two of the three advanced texture feature extraction methods, namely steerable pyramids and LBPs, can extract feature sets of superior quality, when compared to the baseline GLCM and wavelet methods in these three case studies. The application of steerable pyramids and LBPs to further image analysis data sets is therefore recommended as a viable alternative to the traditional GLCM and wavelet texture analysis methods.AFRIKAANSE OPSOMMING: Die meting van sleutelproseskwaliteitsveranderlikes is belangrik vir die doeltreffende en ekono-miese werking van baie chemiese– en mineraalprosesseringsisteme, aangesien hierdie verander-likes gebruik kan word in prosesmonitering– en beheerstelsels om die optimale prosestoestande te identifiseer en te handhaaf. In baie ingenieursprosesse kan die sleutelproseskwaliteits-veranderlikes egter nie direk met standaard sensors gemeet word nie. Inferensiële waarneming is die intydse voorspelling van sulke veranderlikes vanaf ander, meetbare prosesveranderlikes deur van ‘n model gebruik te maak. In beeldgebaseerde inferensiële waarneming word visuele prosesdata, in die vorm van beelde of videogrepe, gebruik as insetveranderlikes vir die inferensiële sensor. Hierdie is ‘n gepaste benadering wanneer die verlangde proseskwaliteitsveranderlike met die visuele voorkoms van die proses gekorreleer is. Die inferensiële sensormodel word dan gebaseer op die analise van die beelddata. Tekstuurkenmerkekstraksie is ‘n beeldanalisebenadering waarmee die tekstuur of ruimtelike organisering van die beeldelemente beskryf kan word. Twee tekstuurkenmerkekstraksiemetodes, naamlik die gebruik van grysskaalmede-aanwesigheidsmatrikse (GSMMs) en golfie-analise, is sterk verteenwoordig in ingenieursprosestoepassings van tekstuuranalise. Alhoewel hierdie twee grondlynmetodes steeds algemeen as die beste beskikbare tekstuuranalisemetodes beskou word, is daar sedertdien verskeie nuwer en meer gevorderde metodes ontwikkel, wat beskik oor eienskappe wat teoreties voordele vir hierdie metodes teenoor die grondlynmetodes behoort te verskaf. Meer spesifiek is daar drie gevorderde tekstuuranalisemetodes wat baie aandag in onlangse masjienvisieliteratuur geniet het, maar wat nog nie baie op ingenieursprosesse toegepas is nie: stuurbare piramiedes, tekstons en lokale binêre patrone (LBPs). Die doel van hierdie studie was om die gebruik van gevorderde tekstuuranalisemetodes te vergelyk met grondlyntekstuuranaliesemetodes vir die voorspelling van sleutelproseskwaliteits-veranderlikes in spesifieke prosesingenieurstoepassings. Drie gevallestudies, waarin tekstuur ‘n belangrike rol behoort te speel, is ondersoek: (i) die voorspelling van platinumgraadklasse vanaf beelde van platinumflottasieskuime, (ii) die voorspelling van fynfraksieklasse vanaf beelde van steenkoolpartikels op ‘n vervoerband, en (iii) die voorspelling van gemiddelde partikelgrootteklasse vanaf beelde van hidrosikloon ondervloeie. Elk van die vyf tekstuurkenmerkstelle is as insette vir twee verskillende klassifiseerders (K-naaste bure en diskriminantanalise) gebruik om die klasse van die uitsetveranderlikes te voorspeel, vir elk van die drie gevallestudies hierbo genoem. Die kwaliteit van die kenmerke wat deur elke metode ge-ekstraheer is, is op ‘n gestruktureerde manier bepaal, gebaseer op hul klassifikasieprestasie na die optimering van die hiperparameters wat verbonde is aan elke metode. In die platinumskuimflottasiegevallestudie het stuurbare piramiedes en LBPs betekenisvol beter as die GSMM–, golfie– en tekstonmetodes presteer. In die steenkoolfynfraksiegevallestudie het die GSMM-metode betekenisvol slegter as al vier ander metodes presteer. Laastens, in die hidrosikloon ondervloeigevallestudie het stuurbare piramiedes en LBPs betekenisvol beter as die GSMM– en golfiemetodes presteer, terwyl die resultaat vir tekstons nie beslissend was nie. Deur al hierdie resultate gesamentlik te beskou, is die oorkoepelende gevolgtrekking gemaak dat twee van die drie gevorderde tekstuurkenmerkekstraksiemetodes, naamlik stuurbare piramiedes en LBPs, hoër kwaliteit kenmerkstelle kan ekstraheer in vergelyking met die GSMM– en golfiemetodes, vir hierdie drie gevallestudies. Die toepassing van stuurbare piramiedes en LBPs op verdere beeldanalise-datastelle word dus aanbeveel as ‘n lewensvatbare alternatief tot die tradisionele GSMM– en golfietekstuuranalisemetodes

Toward data science in biophotonics: biomedical investigations-based study

Biophotonics aims to grasp and investigate the characteristics of biological samples based on their interaction with incident light. Over the past decades, numerous biophotonic technologies have been developed delivering various sorts of biological and chemical information from the studied samples. Such information is usually contained in high dimensional data that need to be translated into high-level information like disease biomarkers. This data translation is not straightforward, but it can be achieved using the advances in computer and data science. The scientific contributions presented in this thesis were established to cover two main aspects of data science in biophotonics: the design of experiments and the data-driven modeling and validation. For the design of experiment, the scientific contributions focus on estimating the sample size required for group differentiation and on evaluating the influence of experimental factors on unbalanced multifactorial designs. Both methods were designed for multivariate data and were checked on Raman spectral datasets. Thereafter, the automatic detection and identification of three diagnostic tasks were checked based on combining several image processing techniques with machine learning (ML) algorithms. In the first task, an improved ML pipeline to predict the antibiotic susceptibilities of E. coli bacteria was presented and evaluated based on bright-field microscopic images. Then, transfer learning-based classification of bladder cancer was demonstrated using blue light cystoscopic images. Finally, different ML techniques and validation strategies were combined to perform the automatic detection of breast cancer based on a small-sized dataset of nonlinear multimodal images. The obtained results exhibited the benefits of data science tools in improving the experimantal planning and the translation of biophotonic-associated data into high-level information for various biophotonic technologies

Intramuscular fat prediction using color and image analysis of bísaro pork breed

This work presents an analytical methodology to predict meat juiciness (discriminant semi-quantitative analysis using groups of intervals of intramuscular fat) and intramuscular fat (regression analysis) in Longissimus thoracis et lumborum (LTL) muscle of Bísaro pigs using as independent variables the animal carcass weight and parameters from color and image analysis. These are non-invasive and non-destructive techniques which allow development of rapid, easy and inexpensive methodologies to evaluate pork meat quality in a slaughterhouse. The proposed predictive supervised multivariate models were non-linear. Discriminant mixture analysis to evaluate meat juiciness by classified samples into three groups—0.6 to 1.1%; 1.25 to 1.5%; and, greater than 1.5%. The obtained model allowed 100% of correct classifications (92% in cross-validation with seven-folds with five repetitions). Polynomial support vector machine regression to determine the intramuscular fat presented R2 and RMSE values of 0.88 and 0.12, respectively in cross-validation with seven-folds with five repetitions. This quantitative model (model’s polynomial kernel optimized to degree of three with a scale factor of 0.1 and a cost value of one) presented R2 and RSE values of 0.999 and 0.04, respectively. The overall predictive results demonstrated the relevance of photographic image and color measurements of the muscle to evaluate the intramuscular fat, rarther than the usual time-consuming and expensive chemical analysis.Work included in the Portuguese PRODER research Project BISOPORC—Pork extensive production of Bísara breed, in two alternative systems: fattening on concentrate vs. chesnut. The CIMO authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support by national funds FCT/MCTES to CIMO (UIDB/00690/2020) and are members of the Healthy Meat network by (CYTED-119RT0568). The CECAV authors are thankful to the project UIDB/CVT/00772/2020 funded by the Foundation for Science and Technology (FCT, Portugal). The authors are grateful to Laboratory of Carcass and Meat Quality of Agriculture School of Polytechnic Institute of Bragança “Cantinho do Alfredo”.UIDB/CVT/00772/2020info:eu-repo/semantics/publishedVersio