Expanding Training Data for Endoscopic Phenotyping of Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic esophageal disorder marked by eosinophil-dominated inflammation. Diagnosing EoE usually involves endoscopic inspection of the esophageal mucosa and obtaining esophageal biopsies for histologic confirmation. Recent advances have seen AI-assisted endoscopic imaging, guided by the EREFS system, emerge as a potential alternative to reduce reliance on invasive histological assessments. Despite these advancements, significant challenges persist due to the limited availability of data for training AI models - a common issue even in the development of AI for more prevalent diseases. This study seeks to improve the performance of deep learning-based EoE phenotype classification by augmenting our training data with a diverse set of images from online platforms, public datasets, and electronic textbooks increasing our dataset from 435 to 7050 images. We utilized the Data-efficient Image Transformer for image classification and incorporated attention map visualizations to boost interpretability. The findings show that our expanded dataset and model enhancements improved diagnostic accuracy, robustness, and comprehensive analysis, enhancing patient outcomes.

Enhanced Feature-based Image Stitching for Endoscopic Videos in Pediatric Eosinophilic Esophagitis

Video endoscopy represents a major advance in the investigation of gastrointestinal diseases. Reviewing endoscopy videos often involves frequent adjustments and reorientations to piece together a complete view, which can be both time-consuming and prone to errors. Image stitching techniques address this issue by providing a continuous and complete visualization of the examined area. However, endoscopic images, particularly those of the esophagus, present unique challenges. The smooth surface, lack of distinct feature points, and non-horizontal orientation complicate the stitching process, rendering traditional feature-based methods often ineffective for these types of images. In this paper, we propose a novel preprocessing pipeline designed to enhance endoscopic image stitching through advanced computational techniques. Our approach converts endoscopic video data into continuous 2D images by following four key steps: (1) keyframe selection, (2) image rotation adjustment to correct distortions, (3) surface unwrapping using polar coordinate transformation to generate a flat image, and (4) feature point matching enhanced by Adaptive Histogram Equalization for improved feature detection. We evaluate stitching quality through the assessment of valid feature point match pairs. Experiments conducted on 20 pediatric endoscopy videos demonstrate that our method significantly improves image alignment and stitching quality compared to traditional techniques, laying a robust foundation for more effective panoramic image creation.

Automatic Image Unfolding and Stitching Framework for Esophageal Lining Video Based on Density-Weighted Feature Matching

Endoscopy is a crucial tool for diagnosing the gastrointestinal tract, but its effectiveness is often limited by a narrow field of view and the dynamic nature of the internal environment, especially in the esophagus, where complex and repetitive patterns make image stitching challenging. This paper introduces a novel automatic image unfolding and stitching framework tailored for esophageal videos captured during endoscopy. The method combines feature matching algorithms, including LoFTR, SIFT, and ORB, to create a feature filtering pool and employs a Density-Weighted Homography Optimization (DWHO) algorithm to enhance stitching accuracy. By merging consecutive frames, the framework generates a detailed panoramic view of the esophagus, enabling thorough and accurate visual analysis. Experimental results show the framework achieves low Root Mean Square Error (RMSE) and high Structural Similarity Index (SSIM) across extensive video sequences, demonstrating its potential for clinical use and improving the quality and continuity of endoscopic visual data.

Circle Representation for Medical Instance Object Segmentation

Recently, circle representation has been introduced for medical imaging, designed specifically to enhance the detection of instance objects that are spherically shaped (e.g., cells, glomeruli, and nuclei). Given its outstanding effectiveness in instance detection, it is compelling to consider the application of circle representation for segmenting instance medical objects. In this study, we introduce CircleSnake, a simple end-to-end segmentation approach that utilizes circle contour deformation for segmenting ball-shaped medical objects at the instance level. The innovation of CircleSnake lies in these three areas: (1) It substitutes the complex bounding box-to-octagon contour transformation with a more consistent and rotation-invariant bounding circle-to-circle contour adaptation. This adaptation specifically targets ball-shaped medical objects. (2) The circle representation employed in CircleSnake significantly reduces the degrees of freedom to two, compared to eight in the octagon representation. This reduction enhances both the robustness of the segmentation performance and the rotational consistency of the method. (3) CircleSnake is the first end-to-end deep instance segmentation pipeline to incorporate circle representation, encompassing consistent circle detection, circle contour proposal, and circular convolution in a unified framework. This integration is achieved through the novel application of circular graph convolution within the context of circle detection and instance segmentation. In practical applications, such as the detection of glomeruli, nuclei, and eosinophils in pathological images, CircleSnake has demonstrated superior performance and greater rotation invariance when compared to benchmarks. The code has been made publicly available: https://github.com/hrlblab/CircleSnake.

Eosinophils Instance Object Segmentation on Whole Slide Imaging Using Multi-label Circle Representation

Eosinophilic esophagitis (EoE) is a chronic and relapsing disease characterized by esophageal inflammation. Symptoms of EoE include difficulty swallowing, food impaction, and chest pain which significantly impact the quality of life, resulting in nutritional impairments, social limitations, and psychological distress. The diagnosis of EoE is typically performed with a threshold (15 to 20) of eosinophils (Eos) per high-power field (HPF). Since the current counting process of Eos is a resource-intensive process for human pathologists, automatic methods are desired. Circle representation has been shown as a more precise, yet less complicated, representation for automatic instance cell segmentation such as CircleSnake approach. However, the CircleSnake was designed as a single-label model, which is not able to deal with multi-label scenarios. In this paper, we propose the multi-label CircleSnake model for instance segmentation on Eos. It extends the original CircleSnake model from a single-label design to a multi-label model, allowing segmentation of multiple object types. Experimental results illustrate the CircleSnake model's superiority over the traditional Mask R-CNN model and DeepSnake model in terms of average precision (AP) in identifying and segmenting eosinophils, thereby enabling enhanced characterization of EoE. This automated approach holds promise for streamlining the assessment process and improving diagnostic accuracy in EoE analysis. The source code has been made publicly available at https://github.com/yilinliu610730/EoE.

Deep Learning-Based Open Source Toolkit for Eosinophil Detection in Pediatric Eosinophilic Esophagitis

Eosinophilic Esophagitis (EoE) is a chronic, immune/antigen-mediated esophageal disease, characterized by symptoms related to esophageal dysfunction and histological evidence of eosinophil-dominant inflammation. Owing to the intricate microscopic representation of EoE in imaging, current methodologies which depend on manual identification are not only labor-intensive but also prone to inaccuracies. In this study, we develop an open-source toolkit, named Open-EoE, to perform end-to-end whole slide image (WSI) level eosinophil (Eos) detection using one line of command via Docker. Specifically, the toolkit supports three state-of-the-art deep learning-based object detection models. Furthermore, Open-EoE further optimizes the performance by implementing an ensemble learning strategy, and enhancing the precision and reliability of our results. The experimental results demonstrated that the Open-EoE toolkit can efficiently detect Eos on a testing set with 289 WSIs. At the widely accepted threshold of >= 15 Eos per high power field (HPF) for diagnosing EoE, the Open-EoE achieved an accuracy of 91%, showing decent consistency with pathologist evaluations. This suggests a promising avenue for integrating machine learning methodologies into the diagnostic process for EoE. The docker and source code has been made publicly available at https://github.com/hrlblab/Open-EoE.