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Miniaturized endoscopy has advanced accurate visual perception within the human body. Prevailing research remains limited to conventional cameras employing convex lenses, where the physical constraints with millimetre-scale thickness impose serious impediments on the micro-level clinical. Recently, with the emergence of meta-optics, ultra-micro imaging based on metalenses (micron-scale) has garnered great attention, serving as a promising solution. However, due to the physical difference of metalens, there is a large gap in data acquisition and algorithm research. In light of this, we aim to bridge this unexplored gap, advancing the novel metalens endoscopy. First, we establish datasets for metalens endoscopy and conduct preliminary optical simulation, identifying two derived optical issues that physically adhere to strong optical priors. Second, we propose MetaScope, a novel optics-driven neural network tailored for metalens endoscopy driven by physical optics. MetaScope comprises two novel designs: Optics-informed Intensity Adjustment (OIA), rectifying intensity decay by learning optical embeddings, and Optics-informed Chromatic Correction (OCC), mitigating chromatic aberration b

Wireless capsule endoscopy (WCE) enables non-invasive visual assessment of the small bowel, but its clinical utility is constrained by the large volume of frames generated per examination and the difficulty of recognising subtle abnormalities under highly variable imaging conditions. Existing learning-based approaches for WCE are predominantly vision-only, often confined to narrow pathology sets, and show limited transfer across datasets and centres. To address these limitations, this study introduces CapCLIP, a domain-specific vision-language representation learning framework for WCE. CapCLIP aligns capsule endoscopy frames with clinically grounded textual descriptions derived from standardised nomenclature and pathology-aware caption templates, thereby learning embeddings that are both semantically informed and transferable. The proposed framework is evaluated against relevant open-source vision and vision-language foundation models under strict zero-shot conditions using unseen WCE datasets. Evaluation covers three downstream tasks: K-nearest neighbour classification, CLIP-style image-text classification, and text-to-image retrieval. Across these settings, CapCLIP consistently o

Endoscopy is essential in medical imaging, used for diagnosis, prognosis and treatment. Developing a robust dynamic 3D reconstruction pipeline for endoscopic videos could enhance visualization, improve diagnostic accuracy, aid in treatment planning, and guide surgery procedures. However, challenges arise due to the deformable nature of the tissues, the use of monocular cameras, illumination changes, occlusions and unknown camera trajectories. Inspired by neural rendering, we introduce NeRFscopy, a self-supervised pipeline for novel view synthesis and 3D reconstruction of deformable endoscopic tissues from a monocular video. NeRFscopy includes a deformable model with a canonical radiance field and a time-dependent deformation field parameterized by SE(3) transformations. In addition, the color images are efficiently exploited by introducing sophisticated terms to learn a 3D implicit model without assuming any template or pre-trained model, solely from data. NeRFscopy achieves accurate results in terms of novel view synthesis, outperforming competing methods across various challenging endoscopy scenes.

Clinical trial studies indicate benefit of watch-and-wait (WW) surveillance for patients with rectal cancer showing a complete or near clinical response (CR) directly after treatment (restaging). However, there are no objectively accurate methods to early detect local tumor regrowth (LR) in patients undergoing WW from follow-up exams. Hence, we developed Temporal Rectal Endoscopy Cross-attention (TREX), a longitudinal deep learning approach that combines pairs of images acquired at restaging and follow-up to distinguish CR from LR. TREX uses pretrained Swin Transformers in a siamese setting to extract features from longitudinal images and dual cross-attention to combine the features without spatial co-registration between image pairs. TREX and Swin-based baselines were trained under two settings: (a) detecting LR or CR at the last available follow-up and (b) early detection of LR at 3--6, 6--12, and 12--24 months before clinical confirmation. TREX achieved the highest accuracy in detecting LR with a high sensitivity of 97% $\pm$ 6% and a balanced accuracy of 90% $\pm$ 3%, and outperformed all baselines in early detection at both 3--6 (74% $\pm$ 1%) and 6--12 months (62% $\pm$ 4%) p

In this document, we describe characteristics and technical details of the multimodal biosignal dataset DOSE-I of procedural sedation for endoscopy published on zenodo. The DOSE-I dataset includes 78.5 hours of recording in 171 records ranging from 6.7 to 70.8 minutes (mean: 27.5, SD: 11.6) of 281 endoscopic procedures. 1129 (median: 6 per record) transitions of consciousness and 7328 (median: 39 per record) individual sedation depth labels were recorded. In addition to clinically annotated biosignals, the DOSE-I dataset provides detailed static data about the respective study subject and metadata about the respective recordings. To further support future research, we provide details about artifact detection and preprocessed pEEG features, too. C code used for this preprocessing is provided separately via Github.

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for machine learning. Despite progress in generating 2D medical images, the complex domain of clinical video generation has largely remained untapped.This paper introduces \model, an innovative approach to generate medical videos that simulate clinical endoscopy scenes. We present a novel generative model design that integrates a meticulously crafted spatial-temporal video transformer with advanced 2D vision foundation model priors, explicitly modeling spatial-temporal dynamics during video generation. We also pioneer the first public benchmark for endoscopy simulation with video generation models, adapting existing state-of-the-art methods for this endeavor.Endora demonstrates exceptional visual quality in generating endoscopy videos, surpassing state-of-the-art methods in extensive testing. Moreover, we explore how this endoscopy simulator can empower downstream video analysis tasks and even generate 3D medical scenes with multi-view consistency. In a nutshell, Endora marks a notable breakthrough in the deployment of generative AI for clinical endoscopy research, se

Pathology detection in Wireless Capsule Endoscopy (WCE) using deep learning has been explored in the recent past. However, deep learning models can be influenced by the color quality of the dataset used to train them, impacting detection, segmentation and classification tasks. In this work, we evaluate the impact of color correction on pathology detection using two prominent object detection models: Retinanet and YOLOv5. We first generate two color corrected versions of a popular WCE dataset (i.e., SEE-AI dataset) using two different color correction functions. We then evaluate the performance of the Retinanet and YOLOv5 on the original and color corrected versions of the dataset. The results reveal that color correction makes the models generate larger bounding boxes and larger intersection areas with the ground truth annotations. Furthermore, color correction leads to an increased number of false positives for certain pathologies. However, these effects do not translate into a consistent improvement in performance metrics such as F1-scores, IoU, and AP50. The code is available at https://github.com/agossouema2011/WCE2024. Keywords: Wireless Capsule Endoscopy, Color correction, Re

In this work, we present EndoDINO, a foundation model for GI endoscopy tasks that achieves strong generalizability by pre-training on a well-curated image dataset sampled from the largest known GI endoscopy video dataset in the literature. Specifically, we pre-trained ViT models with 1B, 307M, and 86M parameters using datasets ranging from 100K to 10M curated images. Using EndoDINO as a frozen feature encoder, we achieved state-of-the-art performance in anatomical landmark classification, polyp segmentation, and Mayo endoscopic scoring (MES) for ulcerative colitis with only simple decoder heads.

Multi-map Sparse Monocular visual Simultaneous Localization and Mapping applied to monocular endoscopic sequences has proven efficient to robustly recover tracking after the frequent losses in endoscopy due to motion blur, temporal occlusion, tools interaction or water jets. The sparse multi-maps are adequate for robust camera localization, however they are very poor for environment representation, they are noisy, with a high percentage of inaccurately reconstructed 3D points, including significant outliers, and more importantly with an unacceptable low density for clinical applications. We propose a method to remove outliers and densify the maps of the state of the art for sparse endoscopy multi-map CudaSIFT-SLAM. The NN LightDepth for up-to-scale depth dense predictions are aligned with the sparse CudaSIFT submaps by means of the robust to spurious LMedS. Our system mitigates the inherent scale ambiguity in monocular depth estimation while filtering outliers, leading to reliable densified 3D maps. We provide experimental evidence of accurate densified maps 4.15 mm RMS accuracy at affordable computing time in the C3VD phantom colon dataset. We report qualitative results on the rea

Abnormalities in the gastrointestinal tract significantly influence the patient's health and require a timely diagnosis for effective treatment. With such consideration, an effective automatic classification of these abnormalities from a video capsule endoscopy (VCE) frame is crucial for improvement in diagnostic workflows. The work presents the process of developing and evaluating a novel model designed to classify gastrointestinal anomalies from a VCE video frame. Integration of Omni Dimensional Gated Attention (OGA) mechanism and Wavelet transformation techniques into the model's architecture allowed the model to focus on the most critical areas in the endoscopy images, reducing noise and irrelevant features. This is particularly advantageous in capsule endoscopy, where images often contain a high degree of variability in texture and color. Wavelet transformations contributed by efficiently capturing spatial and frequency-domain information, improving feature extraction, especially for detecting subtle features from the VCE frames. Furthermore, the features extracted from the Stationary Wavelet Transform and Discrete Wavelet Transform are concatenated channel-wise to capture mul

Capsule endoscopy is a method to capture images of the gastrointestinal tract and screen for diseases which might remain hidden if investigated with standard endoscopes. Due to the limited size of a video capsule, embedding AI models directly into the capsule demands careful consideration of the model size and thus complicates anomaly detection in this field. Furthermore, the scarcity of available data in this domain poses an ongoing challenge to achieving effective anomaly detection. Thus, this work introduces an ensemble strategy to address this challenge in anomaly detection tasks in video capsule endoscopies, requiring only a small number of individual neural networks during both the training and inference phases. Ensemble learning combines the predictions of multiple independently trained neural networks. This has shown to be highly effective in enhancing both the accuracy and robustness of machine learning models. However, this comes at the cost of higher memory usage and increased computational effort, which quickly becomes prohibitive in many real-world applications. Instead of applying the same training algorithm to each individual network, we propose using various loss fu

Wireless capsule endoscopy (WCE) is a non-invasive diagnostic procedure that enables visualization of the gastrointestinal (GI) tract. Deep learning-based methods have shown effectiveness in disease screening using WCE data, alleviating the burden on healthcare professionals. However, existing capsule endoscopy classification methods mostly rely on pre-defined categories, making it challenging to identify and classify out-of-distribution (OOD) data, such as undefined categories or anatomical landmarks. To address this issue, we propose the Endoscopy Out-of-Distribution (EndoOOD) framework, which aims to effectively handle the OOD detection challenge in WCE diagnosis. The proposed framework focuses on improving the robustness and reliability of WCE diagnostic capabilities by incorporating uncertainty-aware mixup training and long-tailed in-distribution (ID) data calibration techniques. Additionally, virtual-logit matching is employed to accurately distinguish between OOD and ID data while minimizing information loss. To assess the performance of our proposed solution, we conduct evaluations and comparisons with 12 state-of-the-art (SOTA) methods using two publicly available datasets

Deep learning can predict depth maps and capsule ego-motion from capsule endoscopy videos, aiding in 3D scene reconstruction and lesion localization. However, the collisions of the capsule endoscopies within the gastrointestinal tract cause vibration perturbations in the training data. Existing solutions focus solely on vision-based processing, neglecting other auxiliary signals like vibrations that could reduce noise and improve performance. Therefore, we propose V$^2$-SfMLearner, a multimodal approach integrating vibration signals into vision-based depth and capsule motion estimation for monocular capsule endoscopy. We construct a multimodal capsule endoscopy dataset containing vibration and visual signals, and our artificial intelligence solution develops an unsupervised method using vision-vibration signals, effectively eliminating vibration perturbations through multimodal learning. Specifically, we carefully design a vibration network branch and a Fourier fusion module, to detect and mitigate vibration noises. The fusion framework is compatible with popular vision-only algorithms. Extensive validation on the multimodal dataset demonstrates superior performance and robustness

Foundation models have become prominent in computer vision, achieving notable success in various tasks. However, their effectiveness largely depends on pre-training with extensive datasets. Applying foundation models directly to small datasets of capsule endoscopy images from scratch is challenging. Pre-training on broad, general vision datasets is crucial for successfully fine-tuning our model for specific tasks. In this work, we introduce a simplified approach called Adapt foundation models with a low-rank adaptation (LoRA) technique for easier customization. Our method, inspired by the DINOv2 foundation model, applies low-rank adaptation learning to tailor foundation models for capsule endoscopy diagnosis effectively. Unlike traditional fine-tuning methods, our strategy includes LoRA layers designed to absorb specific surgical domain knowledge. During the training process, we keep the main model (the backbone encoder) fixed and focus on optimizing the LoRA layers and the disease classification component. We tested our method on two publicly available datasets for capsule endoscopy disease classification. The results were impressive, with our model achieving 97.75% accuracy on th

The images captured by Wireless Capsule Endoscopy (WCE) always exhibit specular reflections, and removing highlights while preserving the color and texture in the region remains a challenge. To address this issue, this paper proposes a highlight removal method for capsule endoscopy images. Firstly, the confidence and feature terms of the highlight region's edges are computed, where confidence is obtained by the ratio of known pixels in the RGB space's R channel to the B channel within a window centered on the highlight region's edge pixel, and feature terms are acquired by multiplying the gradient vector of the highlight region's edge pixel with the iso-intensity line. Subsequently, the confidence and feature terms are assigned different weights and summed to obtain the priority of all highlight region's edge pixels, and the pixel with the highest priority is identified. Then, the variance of the highlight region's edge pixels is used to adjust the size of the sample block window, and the best-matching block is searched in the known region based on the RGB color similarity and distance between the sample block and the window centered on the pixel with the highest priority. Finally,

Video capsule endoscopy has transformed gastrointestinal endoscopy (GIE) diagnostics by offering a non-invasive method for capturing detailed images of the gastrointestinal tract, enabling early disease detection. However, its potential is limited by the sheer volume of images generated during the imaging procedure, which can take anywhere from 6-8 hours and often produce up to 1 million images, necessitating automated analysis. Additionally, the variability of these images, combined with the need for expert annotations and the scarcity of large, high-quality labeled datasets, constrains the effectiveness of current medical image analysis models. To address this, we introduce a novel large GIE dataset, called EndoExtend24, created by merging ten existing public and private datasets, ensuring patient integrity across splits. EndoExtend24 includes over 226,000 labeled images, as well as dynamic class mappings, which allow unified training across datasets with differing labeling granularity, supporting up to 123 distinct pathological findings. Further, we propose to leverage domain adaptive pre-training of foundation models trained with self-supervision on generic image data, to adapt

Accurate 3D mapping in endoscopy enables quantitative, holistic lesion characterization within the gastrointestinal (GI) tract, requiring reliable depth and pose estimation. However, endoscopy systems are monocular, and existing methods relying on synthetic datasets or complex models often lack generalizability in challenging endoscopic conditions. We propose a robust self-supervised monocular depth and pose estimation framework that incorporates a Generative Latent Bank and a Variational Autoencoder (VAE). The Generative Latent Bank leverages extensive depth scenes from natural images to condition the depth network, enhancing realism and robustness of depth predictions through latent feature priors. For pose estimation, we reformulate it within a VAE framework, treating pose transitions as latent variables to regularize scale, stabilize z-axis prominence, and improve x-y sensitivity. This dual refinement pipeline enables accurate depth and pose predictions, effectively addressing the GI tract's complex textures and lighting. Extensive evaluations on SimCol and EndoSLAM datasets confirm our framework's superior performance over published self-supervised methods in endoscopic depth

Automated endoscopy video analysis is a challenging task in medical computer vision, with the primary objective of assisting surgeons during procedures. The difficulty arises from the complexity of surgical scenes and the lack of a sufficient amount of annotated data. In recent years, large-scale pretraining has shown great success in natural language processing and computer vision communities. These approaches reduce the need for annotated data, which is always a concern in the medical domain. However, most works on endoscopic video understanding use models pretrained on natural images, creating a domain gap between pretraining and finetuning. In this work, we investigate the need for endoscopy domain-specific pretraining based on downstream objectives. To this end, we first collect Endo700k, the largest publicly available corpus of endoscopic images, extracted from nine public Minimally Invasive Surgery (MIS) datasets. Endo700k comprises more than 700,000 unannotated raw images. Next, we introduce EndoViT, an endoscopy pretrained Vision Transformer (ViT). Through ablations, we demonstrate that domain-specific pretraining is particularly beneficial for more complex downstream task

In this work for Capsule Vision Challenge 2024, we addressed the challenge of multiclass anomaly classification in video capsule Endoscopy (VCE)[1] with a variety of deep learning models, ranging from custom CNNs to advanced transformer architectures. The purpose is to correctly classify diverse gastrointestinal disorders, which is critical for increasing diagnostic efficiency in clinical settings. We started with a baseline CNN model and improved performance with ResNet[2] for better feature extraction, followed by Vision Transformer (ViT)[3] to capture global dependencies. We further improve the results by using Multiscale Vision Transformer (MViT)[4] for improved hierarchical feature extraction, while Dual Attention Vision Transformer (DaViT) [5] delivered best results by combining spatial and channel attention methods. Our best balanced accuracy on validation set [6] was 0.8592 and Mean AUC was 0.9932. This methodology enabled us to improve model accuracy across a wide range of criteria, greatly surpassing all other methods.Additionally, our team capsule commandos achieved 7th place ranking with a test set[7] performance of Mean AUC: 0.7314 and balanced accuracy: 0.3235