arXiv subjects

Thomas de Lange

Publications and source records attributed to Thomas de Lange.

15 recordsLinked to original sources

arXiv2026

A multi-center analysis of deep learning methods for video polyp detection and segmentation

Colonic polyps are well-recognized precursors to colorectal cancer (CRC), typically detected during colonoscopy. However, the variability in appearance, location, and size of these polyps complicates their detection and removal, leading to challenges in effective surveillance, intervention, and subsequently CRC prevention. The processes of colonoscopy surveillance and polyp removal are highly reliant on the expertise of gastroenterologists and occur within the complexities of the colonic structure. As a result, there is a high rate of missed detections and incomplete removal of colonic polyps, which can adversely impact patient outcomes. Recently, automated methods that use machine learning have been developed to enhance polyps detection and segmentation, thus helping clinical processes and reducing missed rates. These advancements highlight the potential for improving diagnostic accuracy in real-time applications, which ultimately facilitates more effective patient management. Furthermore, integrating sequence data and temporal information could significantly enhance the precision of these methods by capturing the dynamic nature of polyp growth and the changes that occur over time. To rigorously investigate these challenges, data scientists and experts gastroenterologists collaborated to compile a comprehensive dataset that spans multiple centers and diverse populations. This initiative aims to underscore the critical importance of incorporating sequence data and temporal information in the development of robust automated detection and segmentation methods. This study evaluates the applicability of deep learning techniques developed in real-time clinical colonoscopy tasks using sequence data, highlighting the critical role of temporal relationships between frames in improving diagnostic precision.

cs.CV↗

arXiv2025

FocusNet: Transformer-enhanced Polyp Segmentation with Local and Pooling Attention

Colonoscopy is vital in the early diagnosis of colorectal polyps. Regular screenings can effectively prevent benign polyps from progressing to CRC. While deep learning has made impressive strides in polyp segmentation, most existing models are trained on single-modality and single-center data, making them less effective in real-world clinical environments. To overcome these limitations, we propose FocusNet, a Transformer-enhanced focus attention network designed to improve polyp segmentation. FocusNet incorporates three essential modules: the Cross-semantic Interaction Decoder Module (CIDM) for generating coarse segmentation maps, the Detail Enhancement Module (DEM) for refining shallow features, and the Focus Attention Module (FAM), to balance local detail and global context through local and pooling attention mechanisms. We evaluate our model on PolypDB, a newly introduced dataset with multi-modality and multi-center data for building more reliable segmentation methods. Extensive experiments showed that FocusNet consistently outperforms existing state-of-the-art approaches with a high dice coefficients of 82.47% on the BLI modality, 88.46% on FICE, 92.04% on LCI, 82.09% on the NBI and 93.42% on WLI modality, demonstrating its accuracy and robustness across five different modalities. The source code for FocusNet is available at https://github.com/JunZengz/FocusNet.

eess.IV↗

arXiv2025

PolypDB: A Curated Multi-Center Dataset for Development of AI Algorithms in Colonoscopy

Colonoscopy is the primary method for examination, detection, and removal of polyps. However, challenges such as variations among the endoscopists' skills, bowel quality preparation, and the complex nature of the large intestine contribute to high polyp miss-rate. These missed polyps can develop into cancer later, underscoring the importance of improving the detection methods. To address this gap of lack of publicly available, multi-center large and diverse datasets for developing automatic methods for polyp detection and segmentation, we introduce PolypDB, a large scale publicly available dataset that contains 3934 still polyp images and their corresponding ground truth from real colonoscopy videos. PolypDB comprises images from five modalities: Blue Light Imaging (BLI), Flexible Imaging Color Enhancement (FICE), Linked Color Imaging (LCI), Narrow Band Imaging (NBI), and White Light Imaging (WLI) from three medical centers in Norway, Sweden, and Vietnam. We provide a benchmark on each modality and center, including federated learning settings using popular segmentation and detection benchmarks. PolypDB is public and can be downloaded at \url{https://osf.io/pr7ms/}. More information about the dataset, segmentation, detection, federated learning benchmark and train-test split can be found at \url{https://github.com/DebeshJha/PolypDB}.

cs.CV↗

arXiv2023

GastroVision: A Multi-class Endoscopy Image Dataset for Computer Aided Gastrointestinal Disease Detection

Integrating real-time artificial intelligence (AI) systems in clinical practices faces challenges such as scalability and acceptance. These challenges include data availability, biased outcomes, data quality, lack of transparency, and underperformance on unseen datasets from different distributions. The scarcity of large-scale, precisely labeled, and diverse datasets are the major challenge for clinical integration. This scarcity is also due to the legal restrictions and extensive manual efforts required for accurate annotations from clinicians. To address these challenges, we present \textit{GastroVision}, a multi-center open-access gastrointestinal (GI) endoscopy dataset that includes different anatomical landmarks, pathological abnormalities, polyp removal cases and normal findings (a total of 27 classes) from the GI tract. The dataset comprises 8,000 images acquired from Bærum Hospital in Norway and Karolinska University Hospital in Sweden and was annotated and verified by experienced GI endoscopists. Furthermore, we validate the significance of our dataset with extensive benchmarking based on the popular deep learning based baseline models. We believe our dataset can facilitate the development of AI-based algorithms for GI disease detection and classification. Our dataset is available at \url{https://osf.io/84e7f/}.

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arXiv2023

A multi-centre polyp detection and segmentation dataset for generalisability assessment

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as \textit{PolypGen}) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from \url{ https://doi.org/10.7303/syn26376615}.

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arXiv2022

PolypConnect: Image inpainting for generating realistic gastrointestinal tract images with polyps

Early identification of a polyp in the lower gastrointestinal (GI) tract can lead to prevention of life-threatening colorectal cancer. Developing computer-aided diagnosis (CAD) systems to detect polyps can improve detection accuracy and efficiency and save the time of the domain experts called endoscopists. Lack of annotated data is a common challenge when building CAD systems. Generating synthetic medical data is an active research area to overcome the problem of having relatively few true positive cases in the medical domain. To be able to efficiently train machine learning (ML) models, which are the core of CAD systems, a considerable amount of data should be used. In this respect, we propose the PolypConnect pipeline, which can convert non-polyp images into polyp images to increase the size of training datasets for training. We present the whole pipeline with quantitative and qualitative evaluations involving endoscopists. The polyp segmentation model trained using synthetic data, and real data shows a 5.1% improvement of mean intersection over union (mIOU), compared to the model trained only using real data. The codes of all the experiments are available on GitHub to reproduce the results.

eess.IV↗

arXiv2022

SinGAN-Seg: Synthetic training data generation for medical image segmentation

Analyzing medical data to find abnormalities is a time-consuming and costly task, particularly for rare abnormalities, requiring tremendous efforts from medical experts. Artificial intelligence has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. However, the machine learning models used to build these tools are highly dependent on the data used to train them. Large amounts of data can be difficult to obtain in medicine due to privacy, expensive and time-consuming annotations, and a general lack of data samples for infrequent lesions. Here, we present a novel synthetic data generation pipeline, called SinGAN-Seg, to produce synthetic medical images with corresponding masks using a single training image. Our method is different from the traditional GANs because our model needs only a single image and the corresponding ground truth to train. Our method produces alternative artificial segmentation datasets with ground truth masks when real datasets are not allowed to share. The pipeline is evaluated using qualitative and quantitative comparisons between real and synthetic data to show that the style transfer technique used in our pipeline significantly improves the quality of the generated data and our method is better than other state-of-the-art GANs to prepare synthetic images when the size of training datasets are limited. By training UNet++ using both real and the synthetic data generated from the SinGAN-Seg pipeline, we show that models trained with synthetic data have very close performances to those trained on real data when the datasets have a considerable amount of data. In contrast, Synthetic data generated from the SinGAN-Seg pipeline can improve the performance of segmentation models when training datasets do not have a considerable amount of data. The code is available on GitHub.

eess.IV↗

arXiv2022

Visual explanations for polyp detection: How medical doctors assess intrinsic versus extrinsic explanations

Deep learning has in recent years achieved immense success in all areas of computer vision and has the potential of assisting medical doctors in analyzing visual content for disease and other abnormalities. However, the current state of deep learning is very much a black box, making medical professionals highly skeptical about integrating these methods into clinical practice. Several methods have been proposed in order to shine some light onto these black boxes, but there is no consensus on the opinion of the medical doctors that will consume these explanations. This paper presents a study asking medical doctors about their opinion of current state-of-the-art explainable artificial intelligence methods when applied to a gastrointestinal disease detection use case. We compare two different categories of explanation methods, intrinsic and extrinsic, and gauge their opinion of the current value of these explanations. The results indicate that intrinsic explanations are preferred and that explanation.

eess.IV↗

arXiv2022

Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, location, and surface largely affect identification, localisation, and characterisation. Moreover, colonoscopic surveillance and removal of polyps (referred to as polypectomy ) are highly operator-dependent procedures. There exist a high missed detection rate and incomplete removal of colonic polyps due to their variable nature, the difficulties to delineate the abnormality, the high recurrence rates, and the anatomical topography of the colon. There have been several developments in realising automated methods for both detection and segmentation of these polyps using machine learning. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets that come from different centres, modalities and acquisition systems. To test this hypothesis rigorously we curated a multi-centre and multi-population dataset acquired from multiple colonoscopy systems and challenged teams comprising machine learning experts to develop robust automated detection and segmentation methods as part of our crowd-sourcing Endoscopic computer vision challenge (EndoCV) 2021. In this paper, we analyse the detection results of the four top (among seven) teams and the segmentation results of the five top teams (among 16). Our analyses demonstrate that the top-ranking teams concentrated on accuracy (i.e., accuracy > 80% on overall Dice score on different validation sets) over real-time performance required for clinical applicability. We further dissect the methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets.

cs.CV↗

arXiv2021

A Comprehensive Study on Colorectal Polyp Segmentation with ResUNet++, Conditional Random Field and Test-Time Augmentation

Colonoscopy is considered the gold standard for detection of colorectal cancer and its precursors. Existing examination methods are, however, hampered by high overall miss-rate, and many abnormalities are left undetected. Computer-Aided Diagnosis systems based on advanced machine learning algorithms are touted as a game-changer that can identify regions in the colon overlooked by the physicians during endoscopic examinations, and help detect and characterize lesions. In previous work, we have proposed the ResUNet++ architecture and demonstrated that it produces more efficient results compared with its counterparts U-Net and ResUNet. In this paper, we demonstrate that further improvements to the overall prediction performance of the ResUNet++ architecture can be achieved by using conditional random field and test-time augmentation. We have performed extensive evaluations and validated the improvements using six publicly available datasets: Kvasir-SEG, CVC-ClinicDB, CVC-ColonDB, ETIS-Larib Polyp DB, ASU-Mayo Clinic Colonoscopy Video Database, and CVC-VideoClinicDB. Moreover, we compare our proposed architecture and resulting model with other State-of-the-art methods. To explore the generalization capability of ResUNet++ on different publicly available polyp datasets, so that it could be used in a real-world setting, we performed an extensive cross-dataset evaluation. The experimental results show that applying CRF and TTA improves the performance on various polyp segmentation datasets both on the same dataset and cross-dataset.

cs.CV↗

arXiv2021

NanoNet: Real-Time Polyp Segmentation in Video Capsule Endoscopy and Colonoscopy

Deep learning in gastrointestinal endoscopy can assist to improve clinical performance and be helpful to assess lesions more accurately. To this extent, semantic segmentation methods that can perform automated real-time delineation of a region-of-interest, e.g., boundary identification of cancer or precancerous lesions, can benefit both diagnosis and interventions. However, accurate and real-time segmentation of endoscopic images is extremely challenging due to its high operator dependence and high-definition image quality. To utilize automated methods in clinical settings, it is crucial to design lightweight models with low latency such that they can be integrated with low-end endoscope hardware devices. In this work, we propose NanoNet, a novel architecture for the segmentation of video capsule endoscopy and colonoscopy images. Our proposed architecture allows real-time performance and has higher segmentation accuracy compared to other more complex ones. We use video capsule endoscopy and standard colonoscopy datasets with polyps, and a dataset consisting of endoscopy biopsies and surgical instruments, to evaluate the effectiveness of our approach. Our experiments demonstrate the increased performance of our architecture in terms of a trade-off between model complexity, speed, model parameters, and metric performances. Moreover, the resulting model size is relatively tiny, with only nearly 36,000 parameters compared to traditional deep learning approaches having millions of parameters.

eess.IV↗

arXiv2020

Medico Multimedia Task at MediaEval 2020: Automatic Polyp Segmentation

Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in early detection and treatment options, the estimated polyp miss rate is still around 20\%. Support via an automated computer-aided diagnosis system could be one of the potential solutions for the overlooked polyps. Such detection systems can help low-cost design solutions and save doctors time, which they could for example use to perform more patient examinations. In this paper, we introduce the 2020 Medico challenge, provide some information on related work and the dataset, describe the task and evaluation metrics, and discuss the necessity of organizing the Medico challenge.

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arXiv2020

Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy

Gastrointestinal (GI) pathologies are periodically screened, biopsied, and resected using surgical tools. Usually the procedures and the treated or resected areas are not specifically tracked or analysed during or after colonoscopies. Information regarding disease borders, development and amount and size of the resected area get lost. This can lead to poor follow-up and bothersome reassessment difficulties post-treatment. To improve the current standard and also to foster more research on the topic we have released the ``Kvasir-Instrument'' dataset which consists of $590$ annotated frames containing GI procedure tools such as snares, balloons and biopsy forceps, etc. Beside of the images, the dataset includes ground truth masks and bounding boxes and has been verified by two expert GI endoscopists. Additionally, we provide a baseline for the segmentation of the GI tools to promote research and algorithm development. We obtained a dice coefficient score of 0.9158 and a Jaccard index of 0.8578 using a classical U-Net architecture. A similar dice coefficient score was observed for DoubleUNet. The qualitative results showed that the model did not work for the images with specularity and the frames with multiple instruments, while the best result for both methods was observed on all other types of images. Both, qualitative and quantitative results show that the model performs reasonably good, but there is a large potential for further improvements. Benchmarking using the dataset provides an opportunity for researchers to contribute to the field of automatic endoscopic diagnostic and therapeutic tool segmentation for GI endoscopy.

physics.med-ph↗

arXiv2019

ResUNet++: An Advanced Architecture for Medical Image Segmentation

Accurate computer-aided polyp detection and segmentation during colonoscopy examinations can help endoscopists resect abnormal tissue and thereby decrease chances of polyps growing into cancer. Towards developing a fully automated model for pixel-wise polyp segmentation, we propose ResUNet++, which is an improved ResUNet architecture for colonoscopic image segmentation. Our experimental evaluations show that the suggested architecture produces good segmentation results on publicly available datasets. Furthermore, ResUNet++ significantly outperforms U-Net and ResUNet, two key state-of-the-art deep learning architectures, by achieving high evaluation scores with a dice coefficient of 81.33%, and a mean Intersection over Union (mIoU) of 79.27% for the Kvasir-SEG dataset and a dice coefficient of 79.55%, and a mIoU of 79.62% with CVC-612 dataset.

eess.IV↗

arXiv2019

Kvasir-SEG: A Segmented Polyp Dataset

Pixel-wise image segmentation is a highly demanding task in medical-image analysis. In practice, it is difficult to find annotated medical images with corresponding segmentation masks. In this paper, we present Kvasir-SEG: an open-access dataset of gastrointestinal polyp images and corresponding segmentation masks, manually annotated by a medical doctor and then verified by an experienced gastroenterologist. Moreover, we also generated the bounding boxes of the polyp regions with the help of segmentation masks. We demonstrate the use of our dataset with a traditional segmentation approach and a modern deep-learning based Convolutional Neural Network (CNN) approach. The dataset will be of value for researchers to reproduce results and compare methods. By adding segmentation masks to the Kvasir dataset, which only provide frame-wise annotations, we enable multimedia and computer vision researchers to contribute in the field of polyp segmentation and automatic analysis of colonoscopy images.

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