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EndoMapper: Real-time mapping from endoscopic video

Deliverables

DefSLAM in tubular topology (Report)

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)

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

(Nr)SfM for labeling matches in real endoscopies (Report)

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

Unsupervised data association in endoscopy (Report)

Selfsupervised FullyConvolutional Neural Networks based models for correspondence in endoscopies report

Labelling deformation in endoscopies (Report)

Simulated data generation and augmentation framework, report.

Isometric NRSfM for the tubular topology (Report)

Articles for isometric NRSfM, taking point correspondences as inputs.

Non-linear refinement for tubular topology (Report)

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

Def SLAM (Report)

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

EndoMapper challenges, typical use cases

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

Website and Logo

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

Publications

LightNeuS: Neural Surface Reconstruction in Endoscopy using Illumination Decline

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

SD-DefSLAM: Semi-Direct Monocular SLAM for Deformable and Intracorporeal Scenes

Author(s): Juan J. Gómez Rodríguez, José Lamarca, Javier Morlana, Juan D. Tardós, José M. M. Montiel
Published in: arXiv e-prints (submitted to IEEE Int. Conference on Robotics and Automation), 2020
Publisher: IEEE

Structure-from-motion analysis may generate an accurate automated bowel preparation score.

Author(s): Chadebecq F., Mountney P., Ahmad O. F., Kader R., Lovat L. B., Stoyanov D.
Published in: UEG Journal. Abstract Issue, 2020, Page(s) 765
Publisher: SAGE

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

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

On the Uncertain Single-View Depths in Endoscopies

Author(s): Javier Rodríguez-Puigvert, David Recasens, Javier Civera, Rubén Martínez-Cantín
Published in: Medical Image Computing and Computer Assisted Intervention, 2022
Publisher: MICCAI 2022
DOI: 10.48550/arxiv.2112.08906

SD-DefSLAM: Semi-Direct Monocular SLAM for Deformable and Intracorporeal Scenes

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

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

Author(s): Rodríguez-Puigvert, Javier; Batlle, Víctor M.; Montiel, J. M. M.; Martinez-Cantin, Ruben; Fua, Pascal; Tardós, Juan D.; Civera, Javier
Published in: IEEE/CVF International Conference on Computer Vision (ICCV), 2023, Page(s) 21273-21283
Publisher: Computer Vision Foundation
DOI: 10.48550/arxiv.2308.10525

Tracking monocular camera pose and deformation for SLAM inside the human body

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

Author(s): Abhinav Joshi; Naman Gupta; Jinang Shah; Binod Bhattarai; Ashutosh Modi; Danail Stoyanov
Published in: Crossref, Issue 48, 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

Cálculo de flujo óptico denso en colonoscopia mediante aprendizaje no supervisado

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

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

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

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

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

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

Exploring Intra- and Inter-Video Relation for Surgical Semantic Scene Segmentation

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

DefSLAM: Tracking and Mapping of Deforming Scenes From Monocular Sequences

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

Endo-Depth-and-Motion: Reconstruction and tracking in endoscopic videos using depth networks and photometric constraints

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

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

Direct and Sparse Deformable Tracking

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

Colonoscopic 3D reconstruction by tubular non-rigid structure-from-motion

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

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