Superpixel | Zakia Khatun

Advancing Human Soft Tissue Pathology Assessment Using Artificial Intelligence in Medical Imaging

Sat, 01 Feb 2025 00:00:00 +0000

Abstract

Artificial Intelligence (AI) has revolutionized various fields by automating complex tasks, uncovering patterns in large datasets, and making accurate predictions. Machine learning, particularly deep learning, plays a pivotal role in enabling AI to emulate human intelligence for tasks such as image segmentation, classification, and recognition. In the realm of medical imaging, modalities like Magnetic Resonance Imaging (MRI), Computed Tomography (CT), and Ultrasound are indispensable tools for diagnosing pathologies, detecting abnormalities, guiding treatment plans, and monitoring disease progression. The integration of AI with medical imaging offers the potential to enhance the accuracy and efficiency of these processes.

In particular, AI’s application in the assessment of tendon-related conditions, such as tendinopathy, presents a promising avenue for improving patient care. Tendinopathy can significantly impact a patient’s quality of life, and early detection is crucial to optimize treatment outcomes. This thesis focuses on the development of advanced AI-driven methods for analyzing human soft tissue pathologies, with a primary emphasis on tendon segmentation, pathology detection (classification), and tendon reflex response assessment. By automating the analysis of tendons and other human soft tissues, these methods aim to reduce human error and variability, thereby enabling more consistent and reliable clinical decisions. Ultimately, the goal is to support earlier, more accurate diagnoses and interventions, leading to better patient outcomes and more personalized treatment strategies.

This thesis begins with a study that analyzes MRI and CT scans from 47 participants to investigate the relationships between the tendons, cartilage, and muscles in the knee. This study has two primary objectives - first, to predict knee cartilage degeneration, and second, to predict patellar tendinopathy. For both objectives, predictions are made using features extracted solely from the patellar tendon and quadriceps, rather than directly from the cartilage itself. This approach explores the potential of using features from surrounding tissues as indirect predictors of knee-related pathologies. This study demonstrates that both knee cartilage degeneration and patellar tendinopathy can be predicted using these features from adjacent structures, highlighting the importance of surrounding tissues as potential indicators of pathology. Traditional machine learning models are employed to identify the most relevant features for each prediction task, highlighting their importance in the diagnosis of these conditions. This foundational research deepens our understanding of the interrelationships between knee soft tissues, contributing to more accurate diagnostic approaches in musculoskeletal health and enhancing clinical decision-making and treatment strategies.

A central focus of this thesis is the development of an end-to-end tendon segmentation module. This system integrates a superpixel-based coarse segmentation step that serves as a foundation for the final, more precise segmentation. In this approach, the segmentation task is framed as a superpixel classification problem. To achieve this, two distinct approaches are developed - (1) Random Forest (RF) and Support Vector Machine (SVM) classifiers for superpixel categorization, and (2) a Graph Convolutional Network (GCN) for transforming superpixels into graph structures for node classification. The RF and SVM classifiers demonstrate exceptional performance, achieving Area Under the Curve (AUC) scores of 0.992 and 0.987, respectively, with high sensitivity, indicating their effectiveness in accurately classifying superpixels. Although the GCN approach yields slightly lower performance, it showcases the potential of deep learning methods for improving segmentation by leveraging the structural relationships between superpixels. The findings suggest that both traditional machine learning and deep learning techniques offer promising avenues for advancing tendon segmentation, with superpixel-based methods offering a pathway to more reliable and automated segmentation in medical imaging.

Another key component of this thesis is the development of an end-to-end tendon pathology detection module, utilizing the same MRI dataset. This module adopts a graph-based approach, where superpixels are treated as nodes and connected by edge relationships. Each MRI scan is transformed into a graph, with the task framed as a graph classification problem to determine the presence or absence of pathology. To achieve this, a Graph Echo State Network (GESN) is employed. Known for its ability to efficiently represent data without the need for iterative backpropagation, the GESN leverages both temporal and structural dependencies in the data, enhancing classification performance. In this study, the GESN outperforms traditional machine learning models, achieving a mean accuracy of 0.953 and a sensitivity of 0.943. These results underscore the potential of the GESN to significantly enhance diagnostic accuracy, offering a powerful tool for early detection and clinical decision-making in tendon pathology assessment. Moreover, the GESN’s ability to handle complex, high-dimensional data suggests its broad applicability to other medical imaging tasks, further expanding its potential clinical utility.

The final study of this thesis explores the impact of demographic factors, including age, height, weight, and gender, on reflex response times in healthy individuals. This analysis is based on electromyography (EMG) recordings from 40 participants. The results reveal that elderly individuals, particularly those who are taller, heavier, and male, exhibit delayed reflex onsets. Even after normalizing for height, older participants still demonstrate slower reflex responses. These findings highlight the role of demographic factors in neuromuscular reflexes, aiding in the diagnosis and early detection of related disorders.

In conclusion, this research demonstrates the potential of AI, particularly superpixel-based and graph-based models, to advance tendon pathology assessment and exploratory tendon reflex studies, leading to better patient outcomes and musculoskeletal health management.

Graph Echo State Network for MRI-based Tendon Pathology Classification

Wed, 01 Jan 2025 00:00:00 +0000

Background and Objective:

Diagnosing tendon-related pathologies is crucial for early diagnosis and effective treatment planning, enabling timely interventions that can significantly improve patient outcomes.

Methods:

This study presents an end-to-end tendon pathology detection (classification) module utilizing a custom ankle MRI dataset comprising 76 subjects (45 healthy, 31 pathological). We propose a graph-based module that converts images into graph representations for classification. Superpixels are first generated by grouping pixels with similar intensity values, serving as the graph’s nodes, while edges connect neighboring superpixels to establish the graph structure. Next, a Graph Echo State Network (GESN) is employed for classification, leveraging its echo state property that eliminates the need for iterative backpropagation. This property produces rich graph embeddings which are fed into a linear readout layer, where weights and biases are learned using ridge regression with regularization. For baseline comparison, a non-graph-based module extracts radiomic features from both the entire image and individual superpixels, employing four traditional machine learning classifiers. We analyze and compare the performance of the graph-based and non-graph-based modules, using majority voting on slice-level predictions to generate subject-wise predictions.

Results:

Our baseline non-graph-based module achieved relatively better performance by extracting global radiomic features from entire images compared to local features derived from superpixels. In contrast, our graph-based module effectively integrates both local and global perspectives. The graph embeddings produced by the Graph Echo State Network (GESN) enhance data representation, resulting in a mean accuracy of 0.953 ± 0.013 and a mean sensitivity of 0.943 ± 0.035, both significantly surpassing the baseline performance. Additionally, hyperparameters such as the reservoir spectral radius and scaling factors had a notable impact on the outcomes of the graph-based classification.

Conclusions:

Our findings highlight the effectiveness of graph-based models, particularly GESN, in capturing meaningful representations and improving classification performance in tendon pathology detection.

Beyond pixel Superpixel-based MRI Segmentation through Traditional Machine Learning and Graph Convolutional Network

Fri, 01 Nov 2024 00:00:00 +0000

Background and Objective:

Tendon segmentation is crucial for studying tendon-related pathologies like tendinopathy, tendinosis, etc. This step further enables detailed analysis of specific tendon regions using automated or semi-automated methods. This study specifically aims at the segmentation of Achilles tendon, the largest tendon in the human body.

Methods:

This study proposes a comprehensive end-to-end tendon segmentation module composed of a preliminary superpixel-based coarse segmentation preceding the final segmentation task. The final segmentation results are obtained through two distinct approaches. In the first approach, the coarsely generated superpixels are subjected to classification using Random Forest (RF) and Support Vector Machine (SVM) classifiers to classify whether each superpixel belongs to a tendon class or not (resulting in tendon segmentation). In the second approach, the arrangements of superpixels are converted to graphs instead of being treated as conventional image grids. This classification process uses a graph-based convolutional network (GCN) to determine whether each superpixel corresponds to a tendon class or not.

Results:

All experiments are conducted on a custom-made ankle MRI dataset. The dataset comprises 76 subjects and is divided into two sets: one for training (Dataset 1, trained and evaluated using leave-one-groupout cross-validation) and the other as unseen test data (Dataset 2). Using our first approach, the final test AUC (Area Under the ROC Curve) scores using RF and SVM classifiers on the test data (Dataset 2) are 0.992 and 0.987, respectively, with sensitivities of 0.904 and 0.966. On the other hand, using our second approach (GCN-based node classification), the AUC score for the test set is 0.933 with a sensitivity of 0.899.

Conclusions:

Our proposed pipeline demonstrates the efficacy of employing superpixel generation as a coarse segmentation technique for the final tendon segmentation. Whether utilizing RF, SVM-based superpixel classification, or GCN-based classification for tendon segmentation, our system consistently achieves commendable AUC scores, especially the non-graph-based approach. Given the limited dataset, our graph-based method did not perform as well as non-graph-based superpixel classifications; however, the results obtained provide valuable insights into how well the models can distinguish between tendons and non-tendons. This opens up opportunities for further exploration and improvement.