# EndoMapper dataset of complete calibrated endoscopy procedures

arXiv: https://arxiv.org/abs/2204.14240 · HTML: https://mlsanity.com/paper/2204.14240/

## Key facts

- Cited by 53 papers in the map (data through 14 Oct 2026).
- Builds on 21 of its 58 references that are in the map.
- First posted on arXiv 29 Apr 2022.

## Builds on (most cited first, 21 of 21)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [MobileNetV2: Inverted Residuals and Linear Bottlenecks](https://mlsanity.com/paper/1801.04381/) (2018)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (2016)
- [EfficientNetV2: Smaller Models and Faster Training](https://mlsanity.com/paper/2104.00298/) (2021)
- [ORB-SLAM3: An Accurate Open-Source Library for Visual, Visual-Inertial and Multi-Map SLAM](https://mlsanity.com/paper/2007.11898/) (2020)
- [MegaDepth: Learning Single-View Depth Prediction from Internet Photos](https://mlsanity.com/paper/1804.00607/) (2018)
- [Kvasir-SEG: A Segmented Polyp Dataset](https://mlsanity.com/paper/1911.07069/) (2019)
- [Fine-tuning CNN Image Retrieval with No Human Annotation](https://mlsanity.com/paper/1711.02512/) (2017)
- [Direct Sparse Odometry](https://mlsanity.com/paper/1607.02565/) (2016)
- [D2-Net: A Trainable CNN for Joint Detection and Description of Local Features](https://mlsanity.com/paper/1905.03561/) (2019)
- [LinkNet: Exploiting Encoder Representations for Efficient Semantic Segmentation](https://mlsanity.com/paper/1707.03718/) (2017)
- [Back to the Feature: Learning Robust Camera Localization from Pixels to Pose](https://mlsanity.com/paper/2103.09213/) (2021)
- [TernausNet: U-Net with VGG11 Encoder Pre-Trained on ImageNet for Image Segmentation](https://mlsanity.com/paper/1801.05746/) (2018)
- [Incorporating Temporal Prior from Motion Flow for Instrument Segmentation in Minimally Invasive Surgery Video](https://mlsanity.com/paper/1907.07899/) (2019)
- [Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy](https://mlsanity.com/paper/2011.08065/) (2020)
- [The Double Sphere Camera Model](https://mlsanity.com/paper/1807.08957/) (2018)
- [Heidelberg Colorectal Data Set for Surgical Data Science in the Sensor Operating Room](https://mlsanity.com/paper/2005.03501/) (2020)
- [VR-Caps: A Virtual Environment for Capsule Endoscopy](https://mlsanity.com/paper/2008.12949/) (2020)
- [Bimodal Camera Pose Prediction for Endoscopy](https://mlsanity.com/paper/2204.04968/) (2022)
- [UR2KiD: Unifying Retrieval, Keypoint Detection, and Keypoint Description without Local Correspondence Supervision](https://mlsanity.com/paper/2001.07252/) (2020)

## Built on by (most cited first, 30 of 53)

- [Tracking and Mapping in Medical Computer Vision: A Review](https://mlsanity.com/paper/2310.11475/) (2023)
- [EndoGSLAM: Real-Time Dense Reconstruction and Tracking in Endoscopic Surgeries using Gaussian Splatting](https://mlsanity.com/paper/2403.15124/) (2024)
- [Recent Trends in 3D Reconstruction of General Non-Rigid Scenes](https://mlsanity.com/paper/2403.15064/) (2024)
- [LightNeuS: Neural Surface Reconstruction in Endoscopy using Illumination Decline](https://mlsanity.com/paper/2309.02777/) (2023)
- [SimCol3D -- 3D Reconstruction during Colonoscopy Challenge](https://mlsanity.com/paper/2307.11261/) (2023)
- [LightDepth: Single-View Depth Self-Supervision from Illumination Decline](https://mlsanity.com/paper/2308.10525/) (2023)
- [Endo3R: Unified Online Reconstruction from Dynamic Monocular Endoscopic Video](https://mlsanity.com/paper/2504.03198/) (2025)
- [C3VDv2 -- Colonoscopy 3D video dataset with enhanced realism](https://mlsanity.com/paper/2506.24074/) (2025)
- [Leveraging Near-Field Lighting for Monocular Depth Estimation from Endoscopy Videos](https://mlsanity.com/paper/2403.17915/) (2024)
- [EndoOmni: Zero-Shot Cross-Dataset Depth Estimation in Endoscopy by Robust Self-Learning from Noisy Labels](https://mlsanity.com/paper/2409.05442/) (2024)
- [CudaSIFT-SLAM: multiple-map visual SLAM for full procedure mapping in real human endoscopy](https://mlsanity.com/paper/2405.16932/) (2024)
- [Advancing Dense Endoscopic Reconstruction with Gaussian Splatting-driven Surface Normal-aware Tracking and Mapping](https://mlsanity.com/paper/2501.19319/) (2025)
- [EndoMamba: An Efficient Foundation Model for Endoscopic Videos via Hierarchical Pre-training](https://mlsanity.com/paper/2502.19090/) (2025)
- [SegCol Challenge: Semantic Segmentation for Tools and Fold Edges in Colonoscopy data](https://mlsanity.com/paper/2412.16078/) (2024)
- [Colo-SCRL: Self-Supervised Contrastive Representation Learning for Colonoscopic Video Retrieval](https://mlsanity.com/paper/2303.15671/) (2023)
- [Realistic Surgical Image Dataset Generation Based On 3D Gaussian Splatting](https://mlsanity.com/paper/2407.14846/) (2024)
- [Structure-preserving Image Translation for Depth Estimation in Colonoscopy Video](https://mlsanity.com/paper/2408.10153/) (2024)
- [Topological SLAM in colonoscopies leveraging deep features and topological priors](https://mlsanity.com/paper/2409.16806/) (2024)
- [ColonMapper: topological mapping and localization for colonoscopy](https://mlsanity.com/paper/2305.05546/) (2023)
- [The Drunkard's Odometry: Estimating Camera Motion in Deforming Scenes](https://mlsanity.com/paper/2306.16917/) (2023)
- [Task-guided Domain Gap Reduction for Monocular Depth Prediction in Endoscopy](https://mlsanity.com/paper/2310.01663/) (2023)
- [From Pixels to Polygons: A Survey of Deep Learning Approaches for Medical Image-to-Mesh Reconstruction](https://mlsanity.com/paper/2505.03599/) (2025)
- [EndoMetric: Near-Light Monocular Metric Scale Estimation in Endoscopy](https://mlsanity.com/paper/2410.15065/) (2024)
- [3D Densification for Multi-Map Monocular VSLAM in Endoscopy](https://mlsanity.com/paper/2503.14346/) (2025)
- [PPS-Ctrl: Controllable Sim-to-Real Translation for Colonoscopy Depth Estimation](https://mlsanity.com/paper/2504.17067/) (2025)
- [ColonAdapter: Geometry Estimation Through Foundation Model Adaptation for Colonoscopy](https://mlsanity.com/paper/2511.22250/) (2025)
- [BREATH-VL: Vision-Language-Guided 6-DoF Bronchoscopy Localization via Semantic-Geometric Fusion](https://mlsanity.com/paper/2601.03713/) (2026)
- [RealSynCol: a high-fidelity synthetic colon dataset for 3D reconstruction applications](https://mlsanity.com/paper/2602.08397/) (2026)
- [NRGS-SLAM: Monocular Non-Rigid SLAM for Endoscopy via Deformation-Aware 3D Gaussian Splatting](https://mlsanity.com/paper/2602.17182/) (2026)
- [Acquiring Submillimeter-Accurate Multi-Task Vision Datasets for Computer-Assisted Orthopedic Surgery](https://mlsanity.com/paper/2501.15371/) (2025)

## Abstract (arXiv)

Computer-assisted systems are becoming broadly used in medicine. In endoscopy, most research focuses on the automatic detection of polyps or other pathologies, but localization and navigation of the endoscope are completely performed manually by physicians. To broaden this research and bring spatial Artificial Intelligence to endoscopies, data from complete procedures is needed. This paper introduces the Endomapper dataset, the first collection of complete endoscopy sequences acquired during regular medical practice, making secondary use of medical data. Its main purpose is to facilitate the development and evaluation of Visual Simultaneous Localization and Mapping (VSLAM) methods in real endoscopy data. The dataset contains more than 24 hours of video. It is the first endoscopic dataset that includes endoscope calibration as well as the original calibration videos. Meta-data and annotations associated with the dataset vary from the anatomical landmarks, procedure labeling, segmentations, reconstructions, simulated sequences with ground truth and same patient procedures. The software used in this paper is publicly available.