AI in Medicine and Surgery · Leeds

I build computer vision methods that help clinicians see more inside the body: detecting and measuring disease in endoscopy, reconstructing organs in 3D, and guiding surgeons with augmented reality.

I am an Associate Professor in the School of Computer Science at the University of Leeds, where I founded and lead the AI in Medicine and Surgery (AIMS) group and am a member of the Leeds Cancer Research Centre. My work spans detection, segmentation, depth estimation, image registration, tracking and 3D reconstruction, using both classical and deep learning approaches, and is developed with gastroenterologists and surgeons in the NHS and abroad.

Before Leeds, I was a postdoctoral researcher at the University of Oxford's Department of Engineering Science (2018–2022), designing computer-assisted endoscopy models, and at Heidelberg University and DKFZ (2015–2018), where I developed physics-based deformable registration for 3D reconstruction of ultra-high-resolution brain histology. I received my PhD in image analysis from the Université de Lorraine (2016), on endoscopic video analysis for bladder cancer monitoring, and an MSc in Computer Vision from the Université de Bourgogne.

I have organised the EndoCV challenge series and MICCAI challenges on liver AR (P2ILF), co-organised the CaPTion and DEMI workshops at MICCAI, and served as General Chair of MIUA 2025. I sit on the steering committees of IEEE CBMS and MIUA and on the Royal Society Newton International Fellowships committee.

EPSRC New Investigator Award 2025 AMS Springboard Award 2025 World's Top 2% Scientists 2023–2025

News

  • Two papers accepted at MICCAI 2026: Vis2Reg (landmark-free 3D–2D liver registration) and Bayesian Temporal Pose Networks for laparoscopic tool tracking.

  • Self-supervised monocular depth and pose estimation for endoscopy with latent priors published in IEEE Transactions on Medical Imaging.

  • DRENDS, a depth dataset for robotic endoscopy in dynamic scenes, published in Scientific Data.

  • New EPSRC award: Fibre 3D Endoscopy for Improved Clinical Surveillance; CRUK RadNet Leeds award on multi-modal MRI liver tissue maps.

  • Awarded the EPSRC New Investigator Award for real-time high-fidelity AR in laparoscopic liver resection, and the Academy of Medical Sciences Springboard Award.

  • General Chair of MIUA 2025, hosted in Leeds (15–17 July).

  • Congratulations to Dr Ziang Xu (Oxford) and Dr Xukun Zhang (Fudan) on completing their doctorates.

  • Listed among the Elsevier–Stanford World's Top 2% Scientists.

Research themes

Computational endoscopy

Detection, segmentation and quality assessment in GI endoscopy, with a focus on models that hold up across hospitals, devices and modalities.

PolypGen · EndoCV · TGANet · SSL-CPCD

Surgical vision & AR

Registering preoperative CT/MRI to the live laparoscopic view, tracking instruments, and building data for safer minimally invasive surgery.

P2ILF · Vis2Reg · NeeCo · tool pose

3D reconstruction & depth

Monocular depth, pose and surface reconstruction from endoscopic video to measure lesions and map organs in 3D.

Col3D-MTL · latent-prior depth · DRENDS

Robust & multimodal learning

Self-supervision, domain generalisation, out-of-distribution detection and vision–language models for IBD and cancer risk.

UC scoring · OOD · captioning

Selected publications 2021–2026 · click a figure to enlarge

  • Vis2Reg: Visibility-Aware Landmark-Free Geometric 3D–2D Registration for Liver Laparoscopy

    J Feng, X Zhang, S Farid, S Ali

    MICCAI 2026

    Vis2Reg pipeline: a geometry-only network warps the preoperative liver to the visible intraoperative point cloud using visibility, depth and silhouette consistency.

    arXivPDFScholar

  • Self-supervised Monocular Depth and Pose Estimation for Endoscopy with Latent Priors

    Z Xu, B Li, Y Hu, C Zhang, J East, S Ali, J Rittscher

    IEEE Transactions on Medical Imaging, 2026

    DepthNet with a generative latent bank and a VAE-based PoseNet, trained with reprojection and KL losses.

    arXivPDFScholar

  • NeeCo: Image Synthesis of Novel Instrument States Based on Dynamic and Deformable 3D Gaussian Reconstruction

    T Zeng, J Hu, GL Galindo, S Ali, D Sarikaya, P Valdastri, D Jones

    IEEE Transactions on Medical Imaging, 2025

    From input images to a Gaussian scene reconstruction, novel instrument pose synthesis and automatically labelled renderings.

    arXivPDFScholar

  • An objective comparison of methods for augmented reality in laparoscopic liver resection by preoperative-to-intraoperative image fusion from the MICCAI 2022 challenge

    S Ali, Y Espinel, Y Jin, P Liu, B Güttner, X Zhang, L Zhang, T Dowrick, et al.

    Medical Image Analysis 99, 103371, 202567 citations

    Augmented reality in liver laparoscopy: a 3D model from preoperative CT/MRI is registered to the laparoscopic view to reveal tumour and vessels.

    arXivPDFScholar

  • Multi-task learning with cross-task consistency for improved depth estimation in colonoscopy

    PEC Solano, A Bulpitt, V Subramanian, S Ali

    Medical Image Analysis 99, 103379, 202520 citations

    Col3D-MTL: shared backbone with surface-normal and depth decoders tied by a cross-task consistency loss.

    arXivPDFScholar

  • SSL-CPCD: Self-supervised learning with composite pretext-class discrimination for improved generalisability in endoscopic image analysis

    Z Xu, J Rittscher, S Ali

    IEEE Transactions on Medical Imaging, 202426 citations

    Composite pretext-class discrimination with patch- and image-level contrastive estimators and clustering.

    arXivPDFScholar

  • Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

    S Ali, N Ghatwary, D Jha, E Isik-Polat, G Polat, C Yang, W Li, A Galdran, et al.

    Scientific Reports 14, 2032, 2024131 citations

    EndoCV2021: train on five centres, then test on unseen modality and an unseen centre to measure generalisation.

    arXivPDFScholar

  • A multi-centre polyp detection and segmentation dataset for generalisability assessment (PolypGen)

    S Ali, D Jha, N Ghatwary, S Realdon, R Cannizzaro, OE Salem, et al.

    Scientific Data 10, 75, 2023271 citations

    PolypGen samples from six centres across France, Italy, Norway, the UK and Egypt, with masks and boxes.

    arXivPDFScholar

  • FANet: A feedback attention network for improved biomedical image segmentation

    NK Tomar, D Jha, MA Riegler, HD Johansen, D Johansen, J Rittscher, P Halvorsen, S Ali

    IEEE Trans. Neural Networks and Learning Systems 34(11), 2023335 citations

    FANet feeds the previous epoch's mask back through MixPool blocks to refine segmentation.

    arXivPDFScholar

  • TGANet: Text-guided attention for improved polyp segmentation

    NK Tomar, D Jha, U Bagci, S Ali

    MICCAI 2022330 citations

    TGANet uses polyp count and size as text attributes to guide label attention in the decoder.

    arXivPDFScholar

  • Real-time instance segmentation of surgical instruments using attention and multi-scale feature fusion

    JCÁ Cerón, GO Ruiz, L Chang, S Ali

    Medical Image Analysis 81, 102569, 202264 citations

    YOLACT++-based instrument segmentation with multi-scale feature fusion and attention blocks.

    arXivPDFScholar

  • MSRF-Net: A multi-scale residual fusion network for biomedical image segmentation

    A Srivastava, D Jha, S Chanda, U Pal, HD Johansen, D Johansen, et al.

    IEEE Journal of Biomedical and Health Informatics 26(5), 2021426 citations

    Dual-scale dense fusion (DSDF) blocks exchange features across resolutions inside the MSRF sub-network.

    arXivPDFScholar

  • Real-time polyp detection, localization and segmentation in colonoscopy using deep learning

    D Jha, S Ali, NK Tomar, HD Johansen, D Johansen, J Rittscher, et al.

    IEEE Access 9, 40496–40510, 2021494 citations

    Detection results on Kvasir-SEG from EfficientDet, YOLOv4, Faster R-CNN and RetinaNet against ground truth.

    arXivPDFScholar

  • Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

    S Ali, M Dmitrieva, N Ghatwary, S Bano, G Polat, A Temizel, A Krenzer, et al.

    Medical Image Analysis 70, 102002, 2021237 citations

    EndoCV2020 data: artefact classes (specularity, blur, bubbles…) and disease classes (BE, HGD, cancer, polyp).

    arXivPDFScholar

All publications 93 papers · 2021–2026

PaperCited

2026 18

  1. Infrared spectroscopy with statistical analysis and machine learning for cancer risk assessment in inflammatory bowel disease patients

    E Kumi-Barimah, R Toman, A Jha, S Ali, V Subramanian

    Analyst Scholar

    –

  2. LUX: A Lesion-Aware Graph-Conditioned Visual-Language Architecture for Explainable Endoscopic Captioning

    AI Escamilla-Lopez, G Ochoa-Ruiz, S Hinojosa, S Ali

    arXiv preprint arXiv:2608.23853 arXivScholar

    –

  3. A Dataset for Depth in Robotic Endoscopy with Dynamic Scenarios (DRENDS)

    G Loza-Galindo, M Magro, B Calmé, J Hu, E Ruffaldi, D Jones, E De Momi, et al.

    Scientific Data 13 (1), 1163 Scholar

    –

  4. Vis2Reg: Visibility-Aware Landmark-Free Geometric 3D–2D Registration for Liver Laparoscopy

    J Feng, X Zhang, S Farid, S Ali

    MICCAI 2026 arXivScholar

    –

  5. Bayesian Temporal Pose Networks for Uncertainty-Calibrated Laparoscopic Tool Pose Tracking

    O Choudhry, S Ali, CS Biyani, D Jones

    MICCAI 2026 Scholar

    –

  6. DBMF: A Dual-Branch Multimodal Framework for Out-of-Distribution Detection

    J Yue, D Treanor, V Subramanian, S Ali

    arXiv preprint arXiv:2604.08261 arXivScholar

    –

  7. Self-Supervised Vision Transformer for Surgical Phase Recognition in Endoscopic Submucosal Dissection

    G Dutta, A Hammad, T Archer, Q Dou, N Mohammed, S Ali

    IEEE ISBI 2026 Scholar

    –

  8. Patchsurg: Leveraging Synthetic Datasets for High-Fidelity Depth Estimation in Surgery

    Z Xu, C Zhang, J Rittscher, S Ali

    IEEE ISBI 2026 Scholar

    –

  9. GeoTranMesh: a geometry-guided multi-branch mesh transformer for 3D liver segmentation

    J Feng, X Zhang, S Farid, S Ali

    Int. J. Computer Assisted Radiology and Surgery Scholar

    1

  10. Self-supervised ultrasound-video segmentation with feature prediction and 3D localised loss

    E Ellis, R Mendel, A Bulpitt, N Parsa, MF Byrne, S Ali

    Medical Imaging 2026: Image Processing (SPIE) 13925 arXivScholar

    3

  11. A comprehensive multimodal dataset and benchmark for ulcerative colitis scoring in endoscopy

    N Ghatwary, J Yue, A Elgendy, H Nagdy, A Galal, H Fathy, H El-Amin, et al.

    arXiv preprint arXiv:2603.14559 arXivScholar

    4

  12. Self-supervised Monocular Depth and Pose Estimation for Endoscopy with Latent Priors

    Z Xu, B Li, Y Hu, C Zhang, J East, S Ali, J Rittscher

    IEEE Transactions on Medical Imaging arXivScholar

    7

  13. A multi-center analysis of deep learning methods for video polyp detection and segmentation

    N Ghatwary, PC Solano, MR Ibrahim, A Krenzer, F Puppe, S Realdon, et al.

    arXiv preprint arXiv:2603.04288 arXivScholar

    –

  14. Automatic evaluation for knee angle measurement

    S Hiyama, PE Chavarrias, S Ali, RP Rao, T Takahashi, V Shetty, J Tandel, et al.

    Journal of Orthopaedic Reports, 100904 Scholar

    –

  15. General Surgery 4.0 – A Systematic Review of Extended Reality Interventions in General Surgery

    MR Kowal, T Williams, A Dosis, S Pathak, S Farid, DD Stocken, P Lodge, et al.

    Surgical Innovation Scholar

    1

  16. DEnPL: Improved Classification in Imbalanced Medical Datasets via Data-Engineered Prototypical Metric Loss

    Z Wang, W Zang, Y Yuan, S Ali

    MLMI 2025 (MICCAI Workshop) Scholar

    –

  17. Liver mask-guided SAM-enhanced dual-decoder network for landmark segmentation in AR-guided surgery

    X Zhang, S Ali, Y Kang, J Zhu, M Han, L Wang, X Wang, L Zhang

    Int. J. Computer Assisted Radiology and Surgery 21 (1), 115–124 Scholar

    3

  18. A Self-Supervised Framework for Improved Generalisability in Ultrasound B-mode Image Segmentation

    E Ellis, A Bulpitt, N Parsa, MF Byrne, S Ali

    Biomedical Signal Processing and Control arXivScholar

    6

2025 21

  1. NeeCo: Image Synthesis of Novel Instrument States Based on Dynamic and Deformable 3D Gaussian Reconstruction

    T Zeng, J Hu, GL Galindo, S Ali, D Sarikaya, P Valdastri, D Jones

    IEEE Transactions on Medical Imaging arXivScholar

    1

  2. Real-Time Tool Detection in Laparoscopic Datasets for Surgical Training in Low-Resource Settings

    O Choudhry, S Ali, CS Biyani, D Jones

    Healthcare Technology Letters 12 (1), e70045 Scholar

    6

  3. RobustSurg: Tackling domain generalisation for out-of-distribution surgical scene segmentation

    M Ali, M Richards, G Ochoa-Ruiz, S Ali

    arXiv preprint arXiv:2512.02188 arXivScholar

    –

  4. Point-Guided Latent Diffusion Model for Novel View Synthesis in Laparoscopic Liver Surgery

    W Tang, T Chen, Y Espinel, S Farid, E Buc, A Bartoli, S Ali

    Healthcare Technology Letters 12 (1), e70032 Scholar

    –

  5. Nested resolution mesh-graph CNN for automated extraction of liver surface anatomical landmarks

    X Zhang, J Feng, P Liu, M Han, Y Kang, J Zhu, L Wang, X Wang, S Ali, et al.

    Medical Image Analysis, 103825 Scholar

    5

  6. Lesion-Aware Visual-Language Fusion for Automated Image Captioning of Ulcerative Colitis Endoscopic Examinations

    AIL Escamilla, G Ochoa, S Ali

    MICCAI Workshop on Data Engineering in Medical Imaging Scholar

    1

  7. ESPNet: edge-aware feature shrinkage pyramid for polyp segmentation

    R Toman, V Subramanian, S Ali

    MICCAI 2025 Scholar

    8

  8. Preoperative to intraoperative deformed liver volumes registration

    T Chen, J Borgars, AN Mohamad Shahir, S Farid, S Ali

    MIUA 2025 Scholar

    –

  9. 7-DoF laparoscopic peg transfer dataset for surgical skill assessment

    O Choudhry, S Ali, R Rajasundaram, CS Biyani, D Jones

    Frontiers in Medical Technology Scholar

    3

  10. Surg-InvNeRF: Invertible NeRF for 3D tracking and reconstruction in surgical vision

    G Loza, J Hu, D Jones, S Ali, P Valdastri

    arXiv preprint arXiv:2508.09681 arXivScholar

    –

  11. EfficientDet with Knowledge Distillation and Instance Whitening for Real-Time and Generalisable Polyp Detection

    R Toman, V Subramanian, S Ali

    MIUA 2025 Scholar

    –

  12. Midline-constrained loss in the anatomical landmark segmentation of 3D liver models

    AK Abbas, A Gallagher, T Vraimakis, J Borgars, AN Mohamad Shahir, et al.

    MIUA 2025 Scholar

    2

  13. Out-of-Distribution Detection in Gastrointestinal Vision by Estimating Nearest Centroid Distance Deficit

    S Pokhrel, S Bhandari, S Ali, T Lambrou, A Nguyen, YR Shrestha, et al.

    MIUA 2025 arXivScholar

    6

  14. Intraoperative segmentation through deep learning and mask post-processing in laparoscopic liver surgery

    J Borgars, J Raja, A Ramakrishnan, AK Abbas, A Gallagher, et al.

    MIUA 2025 Scholar

    2

  15. PolypDINO: Adapting DINOv2 for Domain Generalized Polyp Segmentation

    M Ali, R Toman, G Ochoa-Ruiz, S Ali

    MIUA 2025 Scholar

    2

  16. Two-stream MeshCNN for key anatomical segmentation on the liver surface

    X Zhang, S Ali, M Han, Y Kang, X Wang, L Zhang

    Int. J. Computer Assisted Radiology and Surgery 20 (7) Scholar

    1

  17. Statistical analysis of infrared spectroscopy for diagnosing inflammatory bowel disease-associated cancer

    E Kumi-Barimah, R Toman, S Ali, A Jha, V Subramanian

    European Conference on Biomedical Optics Scholar

    –

  18. Solving the long-tailed distribution problem by exploiting the synergies and balance of different techniques

    Z Wang, T Lassila, S Ali

    arXiv preprint arXiv:2501.13756 arXivScholar

    2

  19. An objective comparison of methods for augmented reality in laparoscopic liver resection by preoperative-to-intraoperative image fusion from the MICCAI2022 challenge

    S Ali, Y Espinel, Y Jin, P Liu, B Güttner, X Zhang, L Zhang, T Dowrick, et al.

    Medical Image Analysis 99, 103371 arXivScholar

    67

  20. Multi-task learning with cross-task consistency for improved depth estimation in colonoscopy

    PEC Solano, A Bulpitt, V Subramanian, S Ali

    Medical Image Analysis 99, 103379 arXivScholar

    20

  21. Validating polyp and instrument segmentation methods in colonoscopy through Medico 2020 and MedAI 2021 Challenges

    D Jha, V Sharma, D Banik, D Bhattacharya, K Roy, SA Hicks, NK Tomar, et al.

    Medical Image Analysis 99, 103307 arXivScholar

    17

2024 11

  1. SSL-CPCD: self-supervised learning with composite pretext-class discrimination for improved generalisability in endoscopic image analysis

    Z Xu, J Rittscher, S Ali

    IEEE Transactions on Medical Imaging arXivScholar

    26

  2. Robust and smooth Couinaud segmentation via anatomical structure-guided point-voxel network

    X Zhang, S Ali, T Liu, X Zhao, Z Cui, M Han, S Ma, J Zhu, Y Kang, L Wang, et al.

    Computers in Biology and Medicine 182, 109202 Scholar

    12

  3. Artificial Intelligence – A Help or Hindrance to Scientific Writing?

    P Kron, S Farid, S Ali, P Lodge

    Annals of Surgery Scholar

    10

  4. Improving NeRF Representation with No Pose Prior for Novel View Synthesis in Colonoscopy

    PE Chavarrias-Solano, B Bhattarai, S Ali

    MICCAI Workshop DEMI 2024 Scholar

    2

  5. Exploring anchor-free object detection models for surgical tool detection: a comparative study of Faster-RCNN, YOLOv4, and CenterNet++

    C Aparicio, C Guerrero, M Ali Teevno, G Ochoa-Ruiz, S Ali

    Mexican International Conference on Artificial Intelligence Scholar

    3

  6. Tackling domain generalization for out-of-distribution endoscopic imaging

    MA Teevno, G Ochoa-Ruiz, S Ali

    MLMI 2024 (MICCAI Workshop) arXivScholar

    2

  7. Ultrasound Image Segmentation and its Evaluation using Various Encoder Architectures

    E Ellis, A Bulpitt, S Ali

    IEEE CBMS 2024 Scholar

    –

  8. Domain generalization for endoscopic image segmentation by disentangling style-content information and superpixel consistency

    MA Teevno, R Martinez-Garcia-Pena, G Ochoa-Ruiz, S Ali

    IEEE CBMS 2024 arXivScholar

    3

  9. Multi-modal detection transformer with data engineering technique to stratify patients with Ulcerative Colitis

    A Lopez, H Valencia, G Ochoa-Ruiz, S Ali

    IEEE CBMS 2024 Scholar

    1

  10. SSTFB: Leveraging self-supervised pretext learning and temporal self-attention with feature branching for real-time video polyp segmentation

    Z Xu, J Rittscher, S Ali

    arXiv preprint arXiv:2406.10200 arXivScholar

    7

  11. Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

    S Ali, N Ghatwary, D Jha, E Isik-Polat, G Polat, C Yang, W Li, A Galdran, et al.

    Scientific Reports 14 (1), 2032 arXivScholar

    131

2023 10

  1. Real-time surgical tool detection with multi-scale positional encoding and contrastive learning

    G Loza, P Valdastri, S Ali

    Healthcare Technology Letters Scholar

    10

  2. FANet: A feedback attention network for improved biomedical image segmentation

    NK Tomar, D Jha, MA Riegler, HD Johansen, D Johansen, J Rittscher, et al.

    IEEE Trans. Neural Networks and Learning Systems 34 (11), 9375–9388 arXivScholar

    335

  3. Bayesian uncertainty-weighted loss for improved generalisability on polyp segmentation task

    RS Stone, PE Chavarrias-Solano, AJ Bulpitt, DC Hogg, S Ali

    Workshop on Clinical Image-Based Procedures arXivScholar

    4

  4. Image captioning for automated grading and understanding of ulcerative colitis

    FH Valencia, D Flores-Araiza, O Cerda, V Subramanian, T De Lange, et al.

    MICCAI Workshop CaPTion 2023 Scholar

    5

  5. Anatomical-aware point-voxel network for Couinaud segmentation in liver CT

    X Zhang, Y Liu, S Ali, X Zhao, M Sun, M Han, T Liu, P Zhai, Z Cui, P Zhang, et al.

    MICCAI 2023 Scholar

    14

  6. Vision transformer-based self-supervised learning for ulcerative colitis grading in colonoscopy

    A Pyatha, Z Xu, S Ali

    MICCAI Workshop DEMI 2023 Scholar

    8

  7. A Client-server Deep Federated Learning for Cross-domain Surgical Image Segmentation

    R Subedi, RR Gaire, S Ali, A Nguyen, D Stoyanov, B Bhattarai

    MICCAI Workshop DEMI 2023 arXivScholar

    9

  8. A multi-centre polyp detection and segmentation dataset for generalisability assessment

    S Ali, D Jha, N Ghatwary, S Realdon, R Cannizzaro, OE Salem, et al.

    Scientific Data 10 (1), 75 arXivScholar

    271

  9. SUPRA: Superpixel Guided Loss for Improved Multi-Modal Segmentation in Endoscopy

    R Martínez-García-Peña, MA Teevno, G Ochoa-Ruiz, S Ali

    CVPR Workshops 2023 arXivScholar

    4

  10. Why is the winner the best?

    M Eisenmann, A Reinke, V Weru, MD Tizabi, F Isensee, TJ Adler, S Ali, et al.

    CVPR 2023 arXivScholar

    52

2022 17

  1. Where do we stand in AI for endoscopic image analysis? Deciphering gaps and future directions

    S Ali

    npj Digital Medicine 5, 184 Scholar

    98

  2. Biomedical image analysis competitions: The state of current participation practice

    M Eisenmann, A Reinke, V Weru, MD Tizabi, F Isensee, TJ Adler, et al.

    arXiv preprint arXiv:2212.08568 arXivScholar

    55

  3. Patch-level instance-group discrimination with pretext-invariant learning for colitis scoring

    Z Xu, S Ali, S Gupta, S Leedham, JE East, J Rittscher

    MLMI 2022 (MICCAI Workshop) arXivScholar

    7

  4. UNet-eVAE: Iterative Refinement Using VAE Embodied Learning for Endoscopic Image Segmentation

    S Gupta, S Ali, Z Xu, B Bhattarai, B Turney, J Rittscher

    MLMI 2022 (MICCAI Workshop) Scholar

    2

  5. Improving artifact detection in endoscopic video frames using deep learning techniques

    PE Chavarrias-Solano, M Ali-Teevno, G Ochoa-Ruiz, S Ali

    Mexican International Conference on Artificial Intelligence Scholar

    1

  6. A semi-supervised Teacher-Student framework for surgical tool detection and localization

    M Ali, G Ochoa-Ruiz, S Ali

    Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization arXivScholar

    21

  7. Real-time instance segmentation of surgical instruments using attention and multi-scale feature fusion

    JCÁ Cerón, GO Ruiz, L Chang, S Ali

    Medical Image Analysis 81, 102569 arXivScholar

    64

  8. Multi-class motion-based semantic segmentation for ureteroscopy and laser lithotripsy

    S Gupta, S Ali, L Goldsmith, B Turney, J Rittscher

    Computerized Medical Imaging and Graphics 101, 102112 arXivScholar

    19

  9. Self-supervised approach for a fully assistive esophageal surveillance: Quality, anatomy and neoplasia guidance

    Z Xu, S Ali, N Celik, A Bailey, B Braden, J Rittscher

    MICCAI Workshop CaPTion 2022 Scholar

    2

  10. Knowledge distillation with a class-aware loss for endoscopic disease detection

    PE Chavarrias-Solano, MA Teevno, G Ochoa-Ruiz, S Ali

    MICCAI Workshop CaPTion 2022 arXivScholar

    7

  11. A comprehensive survey on recent deep learning-based methods applied to surgical data

    M Ali, RMG Pena, GO Ruiz, S Ali

    arXiv preprint arXiv:2209.01435 arXivScholar

    8

  12. TGANet: Text-guided attention for improved polyp segmentation

    NK Tomar, D Jha, U Bagci, S Ali

    MICCAI 2022 arXivScholar

    330

  13. GMSRF-Net: An improved generalizability with global multi-scale residual fusion network for polyp segmentation

    A Srivastava, S Chanda, D Jha, U Pal, S Ali

    ICPR 2022 arXivScholar

    44

  14. Meta-learning with implicit gradients in a few-shot setting for medical image segmentation

    R Khadka, D Jha, S Hicks, V Thambawita, MA Riegler, S Ali, P Halvorsen

    Computers in Biology and Medicine 143, 105227 arXivScholar

    106

  15. Additive angular margin loss and model scaling network for optimised colitis scoring

    Z Xu, S Ali, J East, J Rittscher

    IEEE ISBI 2022 Scholar

    3

  16. Endoscopic vision challenge 2022

    A Zia, X Liu, K Bhattacharyya, Z Wang, M Berniker, A Jarc, C Nwoye, et al.

    MICCAI 2022 Scholar

    6

  17. Endoscopic computer vision challenges 2.0

    S Ali, NM Ghatwary

    EndoCV @ ISBI 2022 Scholar

    8

2021 16

  1. MSRF-Net: A multi-scale residual fusion network for biomedical image segmentation

    A Srivastava, D Jha, S Chanda, U Pal, HD Johansen, D Johansen, et al.

    IEEE J. Biomedical and Health Informatics 26 (5), 2252–2263 arXivScholar

    426

  2. Iterative deep learning for improved segmentation of endoscopic images

    S Ali, NK Tomar

    Nordic Machine Intelligence 1 (1), 38–40 Scholar

    7

  3. Assessing YOLACT++ for real time and robust instance segmentation of medical instruments in endoscopic procedures

    JCÁ Cerón, L Chang, GO Ruiz, S Ali

    IEEE EMBC 2021 arXivScholar

    31

  4. EndoUDA: A modality independent segmentation approach for endoscopy imaging

    N Celik, S Ali, S Gupta, B Braden, J Rittscher

    MICCAI 2021 arXivScholar

    21

  5. A pilot study on automatic three-dimensional quantification of Barrett's esophagus for risk stratification and therapy monitoring

    S Ali, A Bailey, S Ash, M Haghighat, P Allan, T Ambrose, et al.

    Gastroenterology 161 (3), 865–878 Scholar

    55

  6. Exploring deep learning methods for real-time surgical instrument segmentation in laparoscopy

    D Jha, S Ali, NK Tomar, MA Riegler, D Johansen, HD Johansen, et al.

    IEEE EMBS BHI 2021 arXivScholar

    19

  7. Improved artifact detection in endoscopy imaging through profile pruning

    Z Xu, S Ali, S Gupta, N Celik, J Rittscher

    MIUA 2021 Scholar

    7

  8. Improving Generalizability in Polyp Segmentation using Ensemble Convolutional Neural Network

    NK Tomar, N Ibtehaz, D Jha, P Halvorsen, S Ali

    EndoCV 2021 Workshop Scholar

    3

  9. Spectral endoscopy enhances contrast for neoplasia in surveillance of Barrett's esophagus

    DJ Waterhouse, W Januszewicz, S Ali, RC Fitzgerald, M Di Pietro, et al.

    Cancer Research 81 (12), 3415–3425 Scholar

    34

  10. Real-time polyp segmentation using U-net with IoU loss

    G Batchkala, S Ali

    MediaEval 2021 (CEUR-WS) Scholar

    8

  11. NanoNet: Real-time polyp segmentation in video capsule endoscopy and colonoscopy

    D Jha, NK Tomar, S Ali, MA Riegler, HD Johansen, D Johansen, et al.

    IEEE CBMS 2021 arXivScholar

    107

  12. A comprehensive analysis of classification methods in gastrointestinal endoscopy imaging

    D Jha, S Ali, S Hicks, V Thambawita, H Borgli, PH Smedsrud, T de Lange, et al.

    Medical Image Analysis 70, 102007 Scholar

    72

  13. Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

    S Ali, M Dmitrieva, N Ghatwary, S Bano, G Polat, A Temizel, A Krenzer, et al.

    Medical Image Analysis 70, 102002 arXivScholar

    237

  14. Real-time polyp detection, localization and segmentation in colonoscopy using deep learning

    D Jha, S Ali, NK Tomar, HD Johansen, D Johansen, J Rittscher, et al.

    IEEE Access 9, 40496–40510 arXivScholar

    494

  15. A deep learning framework for quality assessment and restoration in video endoscopy

    S Ali, F Zhou, A Bailey, B Braden, JE East, X Lu, J Rittscher

    Medical Image Analysis 68, 101900 arXivScholar

    198

  16. Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy

    D Jha, S Ali, K Emanuelsen, SA Hicks, E Garcia-Ceja, MA Riegler, et al.

    MultiMedia Modeling (MMM 2021) arXivScholar

    205

Edited proceedings

  • Medical Image Understanding and Analysis: 29th Annual Conference, MIUA 2025, Leeds (Proceedings)

    S Ali, DC Hogg, M Peckham (eds.)

    Springer Nature

  • Cancer Prevention, Detection, and Intervention: CaPTion 2024 (MICCAI Workshop proceedings)

    S Ali, F van der Sommen, BW Papież, N Ghatwary, Y Jin, I Kolenbrander (eds.)

    Springer Nature

  • Cancer Prevention Through Early Detection: CaPTion 2023 (MICCAI Workshop proceedings)

    S Ali, F van der Sommen, M van Eijnatten, BW Papież, Y Jin, et al. (eds.)

    Springer Nature

  • Data Engineering in Medical Imaging: DEMI 2023 (MICCAI Workshop proceedings)

    B Bhattarai, S Ali, A Rau, A Nguyen, A Namburete, R Caramalau, et al. (eds.)

    Springer Nature

  • Cancer Prevention Through Early Detection: CaPTion 2022 (MICCAI Workshop proceedings)

    S Ali, F van der Sommen, BW Papież, M van Eijnatten, Y Jin, et al. (eds.)

    Springer Nature

Patents

  • Quality assessment in video endoscopy

    J Rittscher, S Ali, A Bailey, JE East, B Braden, F Zhou, X Lu

    US Patent 12,249,065

  • Ureteroscopy imaging system and methods

    S Gupta, S Ali, J Rittscher, B Turney, NP Rauniyar, A Ray, et al.

    US Patent App. 18/588,865 and 18/581,220

  • Quantification of Barrett's oesophagus

    S Ali, J Rittscher, B Braden, JE East, A Bailey

    US Patent App. 18/028,796

Funding

£1.41MAwarded since 2024
9Awards
YearsProjectFunderAmount
2025–2028Real-time High-Fidelity Augmented Reality in Laparoscopic Liver ResectionNew Investigator Award · UKRI914EPSRC£739,397
2025–2027Leveraging multi-modality data for targeted biopsy and risk stratification of patients with inflammatory bowel diseaseSpringboard AwardAcademy of Medical Sciences£349,407
2024–2026AI-assisted identification of dysplastic polyps during colonoscopic surveillance in patients with colonic IBDCrohn's & Colitis UK£98,691
2026–2027Fibre 3D Endoscopy for Improved Clinical SurveillanceEPSRC£86,809
2025–2026Holistic 3D vision of the gastrointestinal tract to support clinical decisionsMedTech Place-Based Impact Acceleration AccountEPSRC£46,481
2024–2025Augmented reality in liver laparoscopy leveraging multi-modal imaging dataLeeds BRC Pump-PrimingNIHR£39,890
2026Functional imaging in liver tissue maps with multi-modal MRI and medically informed machine learningRadNet Leeds Development FundCancer Research UK£29,297
2025–2026Artificial Intelligence for Surgical Training Towards Safer and Effective Sub-mucosal DissectionWith Tec de Monterrey and University of ExeterWorldwide Universities Network£10,000
2024Novel robust computer vision methods and synthetic datasets for minimally invasive surgeryWorldwide Universities Network£10,000

Source: ORCID 0000-0003-1313-3542.

Team & opportunities

Graduated doctoral students

  • Dr Ziang XuDPhil, University of Oxford, 2025
  • Dr Xukun ZhangPhD, Fudan University, 2025
  • Dr Soumya GuptaDPhil, University of Oxford, 2022

Open PhD topics

  • Computer vision methods for understanding surgical safety
  • Digital twins for liver cancer using medically informed machine learning
  • Federated learning for multimodal and class-imbalanced healthcare data
  • Image-guided intervention supported with mixed reality
  • Multi-modal endoscopic and surgical AI

Interested in joining AIMS? Email me with your CV and a short note on which topic fits you.