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CORDIS

EndoMapper: Real-time mapping from endoscopic video

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

DefSLAM in tubular topology (Report) (opens in new window)

Intermediate version where the tubular topology of T31 and the iterative nonlinear refinemens of T32 are incorporated The fundamentals and the algorithms are described in the form of articles

Learnt models for depth and deformation (Report) (opens in new window)

Depth estimation model from monocular endoscopic images and initial versions of deformation estimation models report

Generative models for data association (Report) (opens in new window)

Disentangled generative models for learning invariance, report.

Non-isometric NRSfM for the tubular topology (Report) (opens in new window)

Articles for non-isometric NRSfM, taking point correspondences as inputs

(Nr)SfM for labeling matches in real endoscopies (Report) (opens in new window)

(Nr)SfM-based learning of Siamese CNNs for Correspondence, report

Unsupervised data association in endoscopy (Report) (opens in new window)

Selfsupervised FullyConvolutional Neural Networks based models for correspondence in endoscopies report

Labelling deformation in endoscopies (Report) (opens in new window)

Simulated data generation and augmentation framework, report.

Isometric NRSfM for the tubular topology (Report) (opens in new window)

Articles for isometric NRSfM, taking point correspondences as inputs.

Non-linear refinement for tubular topology (Report) (opens in new window)

Articles for nonlinear refinement of the isometric the model taking the point correspondences and an initialization as inputs

Def SLAM (Report) (opens in new window)

The different articles assembled in the report will describe the basis for doing Deformable Visual mapping.

EndoMapper: DL boosted DefSLAM in tubular topology (Report) (opens in new window)

Final version of EndoMapper, report.

End-to-end deformable geometry estimation (Report) (opens in new window)

Joint model for depth and deformation to facilitate integration within the EndoMapper VSLAM pipeline and end-2-end deformable geometry framework, report.

EndoMapper challenges, typical use cases (opens in new window)

Intermediate proof of concept to identify what are the main barriers to overcome during the research

EndoMapper, inspiring use cases (opens in new window)

A final demonstrator intended to communicate the achievements and potential to a broad audience in the last stages of the project.

Website and Logo (opens in new window)

Designing the logo. Create the EndoMapper website in the .eu domain

Publications

LightNeuS: Neural Surface Reconstruction in Endoscopy using Illumination Decline (opens in new window)

Author(s): Batlle, Víctor M.; Montiel, José M. M.; Fua, Pascal; Tardós, Juan D.
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2023, Issue 14229, 2023, Page(s) 502–512, ISBN 978-3-031-43999-5
Publisher: Springer Nature
DOI: 10.1007/978-3-031-43999-5_48

<b>Ueg</b>Week 2020 Poster Presentations (opens in new window)

Author(s): Chadebecq F, Mountney P, Ahmad O.F, Kader R., Lovat L. Stoyanov D.
Published in: United European Gastroenterology Journal, Issue 8, 2023, Page(s) 144-887, ISSN 2050-6406
Publisher: Wiley
DOI: 10.1177/2050640620927345

Semantic analysis of real endoscopies with unsupervised learned

Author(s): Óscar Barbed, Cristina Oriol, Pablo Azagra Millán, Ana Cristina Murillo Arnal
Published in: Medical Imaging with Deep Learning 2022, 2022, ISSN 2640-3498
Publisher: MIDL 2022

Reuse your features: unifying retrieval and feature-metric alignment (opens in new window)

Author(s): Javier Morlana; J.M.M. Montiel
Published in: 2023 IEEE International Conference on Robotics and Automation (ICRA 2023), Issue May 29 - June 2, 2023., 2024, Page(s) 6072-6079, ISBN 979-8-3503-2365-8
Publisher: IEEE International Conference on Robotics and Automation
DOI: 10.1109/icra48891.2023.10160501

SD-DefSLAM: Semi-Direct Monocular SLAM for Deformable and Intracorporeal Scenes (opens in new window)

Author(s): Juan J. Gómez Rodríguez, José Lamarca, Javier Morlana, Juan D. Tardós, José M. M. Montiel
Published in: IEEE Inter. Conf. on Robotics and Automation, 2021, Page(s) 5170-5177, ISBN 978-1-7281-9078-5
Publisher: IEEE
DOI: 10.1109/icra48506.2021.9561512

Normal Reconstruction from Specularity in the Endoscopic Setting (opens in new window)

Author(s): Karim Makki; Adrien Bartoli
Published in: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 2023, ISBN 978-1-6654-7358-3
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/isbi53787.2023.10230672

LightDepth: Single-View Depth Self-Supervision from Illumination Decline (opens in new window)

Author(s): Javier Rodríguez-Puigvert, Víctor M. Batlle, J.M.M. Montiel, Ruben Martinez-Cantin, Pascal Fua, Juan D. Tardós, Javier Civera
Published in: 2023 IEEE/CVF International Conference on Computer Vision (ICCV), 2024, Page(s) 21216-21226, ISBN 979-8-3503-0718-4
Publisher: IEEE
DOI: 10.1109/iccv51070.2023.01945

Tracking monocular camera pose and deformation for SLAM inside the human body (opens in new window)

Author(s): Juan J. Gómez Rodríguez; J.M.M. Montiel; Juan D. Tardós
Published in: 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 2022, ISBN 978-1-6654-7927-1
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/iros47612.2022.9981203

Predicting Image Relationships with Image Box Embeddings during Endoscopy

Author(s): Anita Rau, Lourdes Agapito, and Danail Stoyanov
Published in: Conference on New Technologies for Computer and Robot Assisted Surgery 2022, 2022
Publisher: Predicting Image Relationships with Image Box Embeddings during Endoscopy

Generalized Product-of-Experts for Learning Multimodal Representations in Noisy Environments (opens in new window)

Author(s): Abhinav Joshi; Naman Gupta; Jinang Shah; Binod Bhattarai; Ashutosh Modi; Danail Stoyanov
Published in: 2022 International Conference on Multimodal Interaction, 2022, Page(s) 83-93, ISBN 978-1-4503-9390-4
Publisher: Association for Computing Machinery
DOI: 10.1145/3536221.3556596

Efficient tool segmentation for endoscopic videos in the wild

Author(s): Clara Tomasini, Ínigo Alonso, Luis Riazuelo, Ana C Murillo
Published in: Medical Imaging with Deep Learning 2022, 2022
Publisher: MIDL 2022

ColonMapper: topological mapping and localization for colonoscopy (opens in new window)

Author(s): Javier Morlana, Juan D. Tardós, J. M. M. Montiel
Published in: 2024 IEEE International Conference on Robotics and Automation (ICRA), 2024, Page(s) 6329-6336, ISBN 979-8-3503-8457-4
Publisher: IEEE
DOI: 10.1109/icra57147.2024.10610426

The Drunkard’s Odometry: Estimating Camera Motion in Deforming Scenes

Author(s): David Recasens Lafuente, Martin R. Oswald, Marc Pollefeys, Javier Civera
Published in: Advances in Neural Information Processing Systems 36 (NeurIPS 2023), Issue 2023, 2023
Publisher: Neural Information Processing Systems 36 (NeurIPS 2023)

Cálculo de flujo óptico denso en colonoscopia mediante aprendizaje no supervisado (opens in new window)

Author(s): Gonzalo, Ivan; Morlana, Javier; Martínez Montiel, José María
Published in: XLIV Jornadas de Automática., 2023, Page(s) 861-866, ISBN 978-84-9749-860-9
Publisher: Universidade da Coruña. Servizo de Publicacións.
DOI: 10.17979/spudc.9788497498609.861

Using Specularities to Boost Non-Rigid Structure-from-Motion (opens in new window)

Author(s): Agniva Sengupta, Karim Makki, Adrien Bartoli
Published in: 2024 IEEE International Conference on Robotics and Automation (ICRA), 2024, Page(s) 2652-2659, ISBN 979-8-3503-8457-4
Publisher: IEEE
DOI: 10.1109/icra57147.2024.10610803

Self-supervised Visual Place Recognition for Colonoscopy Sequences

Author(s): Javier Morlana, Pablo Azagra, Javier Civera and José M.M. Montiel
Published in: Medical Imaging with Deep Learning (MIDL 2021), 2021
Publisher: MIDL

Photometric single-view dense 3D reconstruction in endoscopy (opens in new window)

Author(s): Víctor M. Batlle; J.M.M. Montiel; Juan D. Tardós
Published in: 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Issue October 23-27, 2022, 2022, Page(s) 4904-4910, ISBN 978-1-6654-7927-1
Publisher: IEEE
DOI: 10.1109/iros47612.2022.9981742

Colonoscopic 3D Reconstruction by Tubular Non-Rigid Structure-from-Motion

Author(s): Agniva Sengupta and Adrien Bartoli
Published in: International Conference on Information Processing in Computer-Assisted Interventions, 2021
Publisher: The 12th International Conference on Information Processing in Computer-Assisted Interventions (IPCAI 2021)

SuperPoint features in endoscopy (opens in new window)

Author(s): Barbed, O. L.; Chadebecq, F.; Morlana, J.; Martínez-Montiel, J. M.; Murillo, A. C.
Published in: Imaging Systems for GI Endoscopy, and Graphs in Biomedical Image Analysis, Issue 13754, 2022, Page(s) 45–55, ISBN 978-3-031-21083-9
Publisher: Springer, Cham
DOI: 10.1007/978-3-031-21083-9_5

Estimación de Escala Absoluta para Structure from Motion en Endoscopio con Fuente de Luz Cercana.

Author(s): Fernandes Araujo, Anyiel; Martínez Montiel, José María
Published in: reponame:Zaguán. Repositorio Digital de la Universidad de Zaragoza, Issue TAZ-TFG-2022-2042, 2022
Publisher: Universidad de Zaragoza, EINA

Estimación de flujo óptico en sistemas con luz y cámara solidarios para endoscopia monocular.

Author(s): Royo Meneses, Diego; Martínez Montiel, José María
Published in: Repositorio Zaguan (Universidad de Zaragoza), Issue TAZ-TFM-2022-034, 2022
Publisher: Universidad de Zaragoza

Extracción de características en imágenes de procedimientos médicos con técnicas de deep learning (Feature extraction on medical images with Deep Learning)

Author(s): Oscar Leon Barbed
Published in: 2020
Publisher: University of Zaragoza

Monocular slam for deformable scenarios

Author(s): J. Lamarca (supervised by J. M. M. Montiel)
Published in: 2021
Publisher: University of Zaragoza

Estimación numérica de las propiedades diferenciales del campo de deformación en SLAM deformable con FlowNet2

Author(s): Royo Meneses, Diego; Martínez Montiel, José María; Lamarca Peiro, José
Published in: Repositorio Zaguan (Universidad de Zaragoza), Issue TAZ-TFG-2020-2342, 2020
Publisher: Universidad de Zaragoza

Estimación de profundidad con redes neuronales profundas en vídeos de endoscopias (Depth estimation with deep neural networks in endoscopy videos)

Author(s): David Recasens
Published in: 2020
Publisher: University of Zaragoza

ToTem NRSfM: Object-Wise Non-rigid Structure-from-Motion with a Topological Template (opens in new window)

Author(s): Agniva Sengupta, Adrien Bartoli
Published in: International Journal of Computer Vision, Issue 132, 2024, Page(s) 2135-2176, ISSN 0920-5691
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11263-023-01923-6

Elliptical specularity detection in endoscopy with application to normal reconstruction (opens in new window)

Author(s): Karim Makki, Kilian Chandelon, Adrien Bartoli
Published in: International Journal of Computer Assisted Radiology and Surgery, Issue 18, 2023, Page(s) 1323-1328, ISSN 1861-6429
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/s11548-023-02904-3

Exploring Intra- and Inter-Video Relation for Surgical Semantic Scene Segmentation (opens in new window)

Author(s): Yueming Jin, Yang Yu, Cheng Chen, Zixu Zhao, Pheng-Ann Heng, Danail Stoyanov
Published in: IEEE Transactions on Medical Imaging, 2022, ISSN 0278-0062
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tmi.2022.3177077

FedDP: Dual Personalization in Federated Medical Image Segmentation (opens in new window)

Author(s): Jiacheng Wang, Yueming Jin, Danail Stoyanov, Liansheng Wang
Published in: IEEE Transactions on Medical Imaging, Issue 43, 2024, Page(s) 297-308, ISSN 0278-0062
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tmi.2023.3299206

SimCol3D — 3D reconstruction during colonoscopy challenge (opens in new window)

Author(s): Anita Rau, Sophia Bano, Yueming Jin, Pablo Azagra, Javier Morlana, Rawen Kader, Edward Sanderson, Bogdan J. Matuszewski, Jae Young Lee, Dong-Jae Lee, Erez Posner, Netanel Frank, Varshini Elangovan, Sista Raviteja, Zhengwen Li, Jiquan Liu, Seenivasan Lalithkumar, Mobarakol Islam, Hongliang Ren, Laurence B. Lovat, José M.M. Montiel, Danail Stoyanov
Published in: Medical Image Analysis, Issue 96, 2024, Page(s) 103195, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2024.103195

Bimodal Camera Pose Prediction for Endoscopy (opens in new window)

Author(s): Anita Rau, Binod Bhattarai, Lourdes Agapito, Danail Stoyanov
Published in: IEEE Transactions on Medical Robotics and Bionics, Issue 5, 2023, Page(s) 978-989, ISSN 2576-3202
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/tmrb.2023.3320267

NR-SLAM: Non-Rigid Monocular SLAM (opens in new window)

Author(s): Juan J. Gómez Rodríguez, José M.M. Montiel, Juan D. Tardós
Published in: IEEE Transactions on Robotics, Issue Early Access, 2024, Page(s) 1-13, ISSN 1552-3098
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tro.2024.3422004

DefSLAM: Tracking and Mapping of Deforming Scenes From Monocular Sequences (opens in new window)

Author(s): Jose Lamarca, Shaifali Parashar, Adrien Bartoli, J. M. M. Montiel
Published in: IEEE Transactions on Robotics, 2020, Page(s) 1-13, ISSN 1552-3098
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tro.2020.3020739

The shading isophotes: Model and methods for Lambertian planes and a point light (opens in new window)

Author(s): Damien Mariyanayagam, Adrien Bartoli
Published in: Computer Vision and Image Understanding, Issue 248, 2024, Page(s) 104135, ISSN 1077-3142
Publisher: Academic Press
DOI: 10.1016/j.cviu.2024.104135

Endo-Depth-and-Motion: Reconstruction and tracking in endoscopic videos using depth networks and photometric constraints (opens in new window)

Author(s): David Recasens, José Lamarca, José M. Fácil, J.M.M. Montiel, and Javier Civera
Published in: IEEE/RSJ International Conference on Intelligent Robots and Systems, 2021, Page(s) 7225-7232, ISSN 2377-3766
Publisher: IEEE
DOI: 10.1109/lra.2021.3095528

Endomapper dataset of complete calibrated endoscopy procedures (opens in new window)

Author(s): Pablo Azagra; Carlos Sostres; Ángel Ferrández; Luis Riazuelo; Clara Tomasini; O. León Barbed; Javier Morlana; David Recasens; Víctor M. Batlle; Juan J. Gómez-Rodríguez; Richard Elvira; Julia López; Cristina Oriol; Javier Civera; Juan D. Tardós; Ana C. Murillo; Angel Lanas; José M. M. Montiel
Published in: Scientific Data, Issue 10:671(2023), 2023, Page(s) 1-16, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-023-02564-7

A Temporal Learning Approach to Inpainting Endoscopic Specularities and Its Effect on Image Correspondence (opens in new window)

Author(s): Rema Daher, Francisco Vasconcelos, Danail Stoyanov
Published in: Medical Image Analysis, Issue 90, 2024, Page(s) 102994, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.102994

Direct and Sparse Deformable Tracking (opens in new window)

Author(s): Jose Lamarca; Juan J. Gomez Rodriguez; Juan D. Tardos; J.M.M. Montiel
Published in: IEEE ROBOTICS AND AUTOMATION LETTERS, Issue 7(4), 2022, Page(s) 11450-11457, ISSN 2377-3766
Publisher: Institute of Electrical and electronics engineers
DOI: 10.1109/lra.2022.3201253

Histogram of Oriented Gradients meet deep learning: A novel multi-task deep network for 2D surgical image semantic segmentation (opens in new window)

Author(s): Binod Bhattarai, Ronast Subedi, Rebati Raman Gaire, Eduard Vazquez, Danail Stoyanov
Published in: Medical Image Analysis, Issue 85, 2024, Page(s) 102747, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.102747

Colonoscopic 3D reconstruction by tubular non-rigid structure-from-motion (opens in new window)

Author(s): Agniva Sengupta and Adrien Bartoli
Published in: International Journal of Computer Assisted Radiology and Surgery, 2021, Page(s) 1237–1241, ISSN 1861-6429
Publisher: International Journal of Computer Assisted Radiology and Surgery
DOI: 10.1007/s11548-021-02409-x

Reconstrucción 3D a escala real a partir de imágenes monoculares de endoscopio

Author(s): Víctor Martínez Batlle (supervised by Juan Domingo Tardós Solano)
Published in: 2021
Publisher: University of Zaragoza

EndoMapper dataset of complete calibrated endoscopy procedures (opens in new window)

Author(s): Pablo Azagra, Carlos Sostres, Ángel Ferrandez, Luis Riazuelo, Clara Tomasini, Oscar León Barbed, Javier Morlana, David Recasens, Victor M. Batlle, Juan J. Gómez-Rodríguez, Richard Elvira, Julia López, Cristina Oriol, Javier Civera, Juan D. Tardós, Ana Cristina Murillo, Angel Lanas, José M.M. Montiel
Published in: 2021
Publisher: arxiv
DOI: 10.7303/syn26707219

CudaSIFT-SLAM: multiple-map visual SLAM for full procedure mapping in real human endoscopy (opens in new window)

Author(s): Richard Elvira, Juan D. Tardós, José M.M. Montiel
Published in: Arxiv, Issue -, 2024
Publisher: Arxiv
DOI: 10.48550/arxiv.2405.16932

On the Uncertain Single-View Depths in Colonoscopies (opens in new window)

Author(s): Javier Rodriguez-Puigvert, David Recasens, Javier Civera, Ruben Martinez-Cantin
Published in: Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention – MICCAI 2022, 2024, Page(s) 130-140, ISBN 978-3-031-16437-8
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-16437-8_13

Tracking Adaptation to Improve SuperPoint for 3D Reconstruction in Endoscopy (opens in new window)

Author(s): O. León Barbed, José M. M. Montiel, Pascal Fua, Ana C. Murillo
Published in: Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention – MICCAI 2023, 2024, Page(s) 583-593
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-43907-0_56

Sim2Real in Endoscopy Segmentation with a Novel Structure Aware Image Translation (opens in new window)

Author(s): Clara Tomasini, Luis Riazuelo, Ana C. Murillo
Published in: Lecture Notes in Computer Science, Simulation and Synthesis in Medical Imaging, Issue LNCS,volume 15187, 2024, Page(s) 89-101, ISBN 978-3-031-73281-2
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-73281-2_9

Topological SLAM in Colonoscopies Leveraging Deep Features and Topological Priors (opens in new window)

Author(s): Javier Morlana, Juan D. Tardós, José M. M. Montiel
Published in: Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention – MICCAI 2024, 2024, Page(s) 733-743, ISBN 978-3-031-72120-5
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72120-5_68

A Client-Server Deep Federated Learning for Cross-Domain Surgical Image Segmentation (opens in new window)

Author(s): Ronast Subedi, Rebati Raman Gaire, Sharib Ali, Anh Nguyen, Danail Stoyanov, Binod Bhattarai
Published in: Lecture Notes in Computer Science, Data Engineering in Medical Imaging, Issue LNCS,volume 14314, 2023, Page(s) 21-33, ISBN 978-3-031-44992-5
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-44992-5_3

Intellectual Property Rights

SD-DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/SD-DefSLAM
Date: 2022-04-05
Applicant(s): UNIVERSIDAD DE ZARAGOZA

DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/DefSLAM
Date: 2020-07-06
Applicant(s): UNIVERSIDAD DE ZARAGOZA

DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/DefSLAM
Date: 2020-07-06
Applicant(s): UNIVERSITE CLERMONT AUVERGNE

Endo-Depth-And-Motion

Application/Publication number: N/A https://github.com/UZ-SLAMLab/Endo-Depth-and-Motion
Date: 2021-03-04
Applicant(s): UNIVERSIDAD DE ZARAGOZA

Endo-Depth-And-Motion

Application/Publication number: N/A https://github.com/UZ-SLAMLab/Endo-Depth-and-Motion
Date: 2021-03-04
Applicant(s): UNIVERSIDAD DE ZARAGOZA

DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/DefSLAM
Date: 2020-07-06
Applicant(s): UNIVERSITE CLERMONT AUVERGNE

DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/DefSLAM
Date: 2020-07-06
Applicant(s): UNIVERSIDAD DE ZARAGOZA

SD-DefSLAM

Application/Publication number: N/A https://github.com/UZ-SLAMLab/SD-DefSLAM
Date: 2022-04-05
Applicant(s): UNIVERSIDAD DE ZARAGOZA

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