Jianning Li

Medical AI Researcher

I develop computational methods at the frontier of medical image analysis, AI, computer vision, and deep learning. My research advances how machines understand and interact with clinical imaging data, from skull reconstruction to dental morphology to intelligent diagnostic pipelines. In particular, my research focuses on deep generative models, explainable AI, and computationally efficient shape-based methods for medical applications, with a strong track record of publications in top journals of his field.

Medical Image Analysis Computer Vision Deep Generative Models Interpretable AI Disentangled Representation Learning
πŸ“Œ

Open to collaborations on papers & grants, research discussions, and Bachelor/Master thesis supervision.

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Background & Education

Jianning Li is a researcher specializing in the application of computer vision and deep learning to medical image analysis. He holds a Ph.D. and M.S. in Computer Science (both with distinction) and a B.S. in Biomedical Engineering (with distinction), reflecting a career built at the unique intersection of engineering and clinical science.

His work develops intelligent systems for analyzing medical imagery, including cranial reconstruction, automated tooth segmentation, root canal morphology, and brain tumor analysis. A core thread throughout his research is clinical translation: building tools that not only advance science but improve care.

Beyond core research, Jianning actively contributes to the scientific community through peer review, workshop organization, and mentoring the next generation of researchers. He is particularly passionate about interpretable AI, models that clinicians can understand, trust, and use.

Education

Ph.D. Computer Science With Distinction
M.S. Computer Science With Distinction
B.S. Biomedical Engineering With Distinction

Latest
Updates

Closed
2024

We were looking for a research student assistant. This position is now closed.

Conference
Oct 2023

Attended MICCAI 2023 in Vancouver, Canada (Oct 8–15).

Collaboration
Ongoing

Actively seeking collaborators for joint papers and grant proposals in AI-powered clinical imaging. Reach out to discuss!

Research
Projects

01

MONAI Skull Reconstruction

Open-source skull reconstruction pipeline built on MONAI. Provides a reproducible, community-friendly framework for cranial implant design.

MONAIOpen Source3D Deep Learning
View Project β†’
02

Sparse CNN for Shape Completion & Super-resolution

Sparse convolutional neural networks for high-resolution skull shape completion and shape super-resolution from low-resolution inputs.

Sparse CNNShape CompletionSuper-resolution
View Project β†’
03

Registration-based Shape Completion

A registration-driven approach to skull shape completion, leveraging image registration to complete missing anatomical regions.

RegistrationShape CompletionSkull
View Project β†’
04

Coarse-to-Fine Shape Completion

A coarse-to-fine (C2F) framework for high-resolution skull shape completion, enabling detailed implant design from CT scans.

C2FHigh-resolutionImplant Design
View Project β†’
05

Cloud Deployment for Shape Completion

Deploying deep learning skull shape completion models to the cloud β€” a practical example of clinical AI deployment.

CloudDeploymentDeep Learning
View Project β†’
06

Patch-wise Skull Reconstruction

Patch-based approach to skull reconstruction, enabling scalable processing of large volumetric CT data for cranioplasty planning.

Patch-wiseSkullReconstruction
View Project β†’

Selected
Publications

2025

Computational Insights into Root Canal Treatment: A Survey of Selected Methods in Imaging, Segmentation, Morphological Analysis, and Clinical Management.

Dentistry Journal, Volume 13, Issue 12 β€” Featured Cover Paper

Li, J., Bitter, K., et al.

2025

MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision.

Biomedical Engineering / Biomedizinische Technik, Volume 70, Issue 1

Li, J., Zhou, Z., Yang, J., Pepe, A., Gsaxner, C., Luijten, G., et al.

2023

Why is the winner the best?

IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), pp. 19955–19966

Eisenmann, M., Reinke, A., …, Li, J., …, et al.

2024

How we won BraTS 2023 Adult Glioma challenge? Just faking it! Enhanced Synthetic Data Augmentation and Model Ensemble for brain tumour segmentation.

BraTS 2023 β€” First Place

Ferreira, A., Solak, N., Li, J., Dammann, P., Kleesiek, J., Alves, V. and Egger, J.

2023

The HoloLens in medicine: A systematic review and taxonomy.

Medical Image Analysis, Volume 85, p. 102757

Gsaxner, C., Li, J., Pepe, A., et al.

2023

Towards clinical applicability and computational efficiency in automatic cranial implant design: An overview of the AutoImplant 2021 cranial implant design challenge.

Medical Image Analysis, Volume 88, August 2023, 102865

Li, J., Ellis, D.G., Kodym, O., Rauschenbach, L., Rieß, et al.

2023

Anatomy Completor: A Multi-class Completion Framework for 3D Anatomy Reconstruction.

International Workshop on Shape in Medical Imaging (ShapeMI 2023), pp. 1–14. Springer.

Li, J., Pepe, A., Luijten, G., Schwarz-Gsaxner, C., et al.

2023

Sparse convolutional neural network for high-resolution skull shape completion and shape super-resolution.

Scientific Reports

Li, J., Gsaxner, C., Pepe, A., et al.

2022

Training Ξ²-VAE by Aggregating a Learned Gaussian Posterior with a Decoupled Decoder.

Medical Applications with Disentanglements (MAD 2022). Springer, Cham.

Li, J., Fragemann, J., et al.

2021

AutoImplant 2020 β€” First MICCAI Challenge on Automatic Cranial Implant Design.

IEEE Transactions on Medical Imaging (TMI), DOI: 10.1109/TMI.2021.3077047

Li, J., Pimentel, P., Szengel, A., Ehlke, M., Lamecker, H., et al.

2021

Automatic Skull Defect Restoration and Cranial Implant Generation for Cranioplasty.

Medical Image Analysis (MedIA), 2021

Li, J., von Campe, G., Pepe, A., Gsaxner, C., et al.

2021

Inside-Out Instrument Tracking for Surgical Navigation in Augmented Reality.

27th ACM Symposium on Virtual Reality Software and Technology, pp. 1–11

Gsaxner, C., Li, J., Pepe, A., Schmalstieg, D. and Egger, J.

2021

An Online Platform for Automatic Skull Defect Restoration and Cranial Implant Design.

Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling, SPIE

Li, J., Pepe, A., Gsaxner, C. and Egger, J.

2020

A Baseline Approach for AutoImplant: The MICCAI 2020 Cranial Implant Design Challenge.

Multimodal Learning for Clinical Decision Support and Clinical Image-Based Procedures, pp. 75–84. Springer, Cham.

Li, J., Pepe, A., Gsaxner, C., von Campe, G. and Egger, J.

2020

Detection, segmentation, simulation and visualization of aortic dissections: A review.

Medical Image Analysis (MedIA), 65, p. 101773

Pepe, A.*, Li, J.* (*Equal contribution), Rolf-Pissarczyk, M., Gsaxner, C., Chen, X., Holzapfel, G.A. and Egger, J.

2020

Medical image segmentation in oral-maxillofacial surgery.

Computer-Aided Oral and Maxillofacial Surgery, pp. 1–27

Li, J., Erdt, M., Janoos, F., Chang, T.C. and Egger, J.

Books &
Proceedings

Shape in Medical Imaging

International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023.

Editor / Organizer View on Springer β†’

Medical Applications with Disentanglements

First MICCAI Workshop, MAD 2022, held in conjunction with MICCAI 2022, Singapore, September 22, 2022.

Editor / Organizer View on Springer β†’

Towards the Automatization of Cranial Implant Design in Cranioplasty II

Second Challenge, AutoImplant 2021, held in conjunction with MICCAI 2021, Strasbourg, France, October 1, 2021.

Editor / Challenge Lead View on Springer β†’

Towards the Automatization of Cranial Implant Design in Cranioplasty I

First Challenge, AutoImplant 2020, held in conjunction with MICCAI 2020, Lima, Peru, October 8, 2020.

Editor / Challenge Lead View on Springer β†’

Presentations
& Talks

2023CCVL Lab @ Johns Hopkins University
20232nd UA-Ruhr Biomedical Image Analysis Graduate Seminar
2023EMBC β€” Coronary Artery Segmentation Workshop
2022MAD Workshop @ MICCAI 2022

VAE-based Skull Shape Completion

Poster Presentation

2022IKIM Talk
2022Wahlfach Klinik β€” Digitale Medizin und KΓΌnstliche Intelligenz
2020AutoImplant Challenge @ MICCAI 2020

Academic
Service

Challenge Lead Organizer

Workshop / Tutorial Co-organizer

Program Committee

Reviewer

  • MICCAI β€” Medical Image Computing & Computer Assisted Intervention
  • Medical Image Analysis (MedIA)
  • IEEE ISBI β€” International Symposium on Biomedical Imaging
  • Computers in Biology and Medicine
  • Artificial Intelligence in Medicine
  • Pattern Recognition Letters

Editorial

Memberships

Teaching &
Mentoring

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Courses Taught

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Thesis Supervision

Offering Bachelor's and Master's thesis topics in:

  • Medical image segmentation
  • Interpretable AI in radiology
  • 3D reconstruction from scans
  • Generative models for augmentation
βœ‰οΈ

Prospective Students

Interested in a thesis or research collaboration? Reach out with your CV and a brief description of your interests.

jianningli.me@gmail.com