EndoSLAM dataset and an unsupervised monocular visual odometry and depth estimation approach for endoscopic videos

Deep learning techniques hold promise to develop dense topography reconstruction and pose estimation methods for endoscopic videos. However, currently available datasets do not support effective quantitative benchmarking. In this paper, we introduce a comprehensive endoscopic SLAM dataset consisting of 3D point cloud data for six porcine organs, capsule and standard endoscopy recordings, synthetically generated data as well as clinically in use conventional endoscope recording of the phantom colon with computed tomography(CT) scan ground truth. A Panda robotic arm, two commercially available capsule endoscopes, three conventional endoscopes with different camera properties, two high precision 3D scanners, and a CT scanner were employed to collect data from eight ex-vivo porcine gastrointestinal (GI)-tract organs and a silicone colon phantom model. In total, 35 sub-datasets are provided with 6D pose ground truth for the ex-vivo part: 18 sub-datasets for colon, 12 sub-datasets for stomach, and 5 sub-datasets for small intestine, while four of these contain polyp-mimicking elevations carried out by an expert gastroenterologist. To verify the applicability of this data for use with real clinical systems, we recorded a video sequence with a state-of-the-art colonoscope from a full representation silicon colon phantom. Synthetic capsule endoscopy frames from stomach, colon, and small intestine with both depth and pose annotations are included to facilitate the study of simulation-to-real transfer learning algorithms. Additionally, we propound Endo-SfMLearner, an unsupervised monocular depth and pose estimation method that combines residual networks with a spatial attention module in order to dictate the network to focus on distinguishable and highly textured tissue regions. The proposed approach makes use of a brightness-aware photometric loss to improve the robustness under fast frame-to-frame illumination changes that are commonly seen in endoscopic videos. To exemplify the use-case of the EndoSLAM dataset, the performance of Endo-SfMLearner is extensively compared with the state-of-the-art: SC-SfMLearner, Monodepth2, and SfMLearner. The codes and the link for the dataset are publicly available at https://github.com/CapsuleEndoscope/EndoSLAM. A video demonstrating the experimental setup and procedure is accessible as Supplementary Video 1.

VR-Caps: A Virtual Environment for Capsule Endoscopy

Current capsule endoscopes and next-generation robotic capsules for diagnosis and treatment of gastrointestinal diseases are complex cyber-physical platforms that must orchestrate complex software and hardware functions. The desired tasks for these systems include visual localization, depth estimation, 3D mapping, disease detection and segmentation, automated navigation, active control, path realization and optional therapeutic modules such as targeted drug delivery and biopsy sampling. Data-driven algorithms promise to enable many advanced functionalities for capsule endoscopes, but real-world data is challenging to obtain. Physically-realistic simulations providing synthetic data have emerged as a solution to the development of data-driven algorithms. In this work, we present a comprehensive simulation platform for capsule endoscopy operations and introduce VR-Caps, a virtual active capsule environment that simulates a range of normal and abnormal tissue conditions (e.g., inflated, dry, wet etc.) and varied organ types, capsule endoscope designs (e.g., mono, stereo, dual and 360^∘ camera), and the type, number, strength, and placement of internal and external magnetic sources that enable active locomotion. VR-Caps makes it possible to both independently or jointly develop, optimize, and test medical imaging and analysis software for the current and next-generation endoscopic capsule systems. To validate this approach, we train state-of-the-art deep neural networks to accomplish various medical image analysis tasks using simulated data from VR-Caps and evaluate the performance of these models on real medical data. Results demonstrate the usefulness and effectiveness of the proposed virtual platform in developing algorithms that quantify fractional coverage, camera trajectory, 3D map reconstruction, and disease classification. All of the code, pre-trained weights and created 3D organ models of the virtual environment with detailed instructions how to setup and use the environment are made publicly available at https://github.com/CapsuleEndoscope/VirtualCapsuleEndoscopy and a video demonstration can be seen in the supplementary videos (Video-I).

EndoL2H: Deep Super-Resolution for Capsule Endoscopy

Although wireless capsule endoscopy is the preferred modality for diagnosis and assessment of small bowel diseases, the poor camera resolution is a substantial limitation for both subjective and automated diagnostics. Enhanced-resolution endoscopy has shown to improve adenoma detection rate for conventional endoscopy and is likely to do the same for capsule endoscopy. In this work, we propose and quantitatively validate a novel framework to learn a mapping from low-to-high-resolution endoscopic images. We combine conditional adversarial networks with a spatial attention block to improve the resolution by up to factors of 8× , 10× , 12× , respectively. Quantitative and qualitative studies demonstrate the superiority of EndoL2H over state-of-the-art deep super-resolution methods Deep Back-Projection Networks (DBPN), Deep Residual Channel Attention Networks (RCAN) and Super Resolution Generative Adversarial Network (SRGAN). Mean Opinion Score (MOS) tests were performed by 30 gastroenterologists qualitatively assess and confirm the clinical relevance of the approach. EndoL2H is generally applicable to any endoscopic capsule system and has the potential to improve diagnosis and better harness computational approaches for polyp detection and characterization. Our code and trained models are available at https://github.com/CapsuleEndoscope/EndoL2H.