Awesome Topology-Driven (Deep) Image Analysis

A curated list of resources for topology-driven (deep) image analysis, inspired by awesome-deep-vision and awesome-computer-vision.

Contributing

Please feel free to pull requests or send me email ([email protected]) to contribute.

Table of Contents

• Books
• Tools
• Software
• Tutorials
• Workshops
• Papers
  • Segmentation
  • Classification
  • Detection
  • Registration
  • Reconstruction
  • Counting
  • Uncertainty Estimation
  • Generative Models
  • Other Topics

Books

• Computational Topology. An Introduction by Herbert Edelsbrunner
• Computational Topology for Data Analysis by Tamal Krishna Dey, and Yusu Wang

Tools

• Persistent homology
• Morse theory

Software

• GUDHI library
• Ripser
• Scikit-TDA

Tutorials

• Topology-Driven Image Analysis

Workshops

• The First Workshop on Topology- and Graph-Informed Imaging Informatics (TGI3)

Papers

Segmentation

• Xiaoling Hu, Fuxin Li, Dimitris Samaras, and Chao Chen. "Topology-preserving deep image segmentation." NeurIPS'2019. [Paper]
• Zuoyue Li, Jan Dirk Wegner, and Aurélien Lucchi. "Topological map extraction from overhead images." ICCV'2019. [Paper]
• Samik Banerjee, Lucas Magee, Dingkang Wang, Xu Li, Bing-Xing Huo, Jaikishan Jayakumar, Katherine Matho et al. "Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder–decoder deep networks." NMI'2020. [Paper]
• Seung Yeon Shin, Sungwon Lee, Daniel Elton, James L. Gulley, and Ronald M. Summers. "Deep small bowel segmentation with cylindrical topological constraints." MICCAI'2020. [Paper]
• James R. Clough, Nicholas Byrne, Ilkay Oksuz, Veronika A. Zimmer, Julia A. Schnabel, Andrew P. King. "A topological loss function for deep-learning based image segmentation using persistent homology." TPAMI'2020. [Paper]
• Xiaoling Hu, Yusu Wang, Li Fuxin, Dimitris Samaras, and Chao Chen. "Topology-aware segmentation using discrete morse theory." ICLR'2021. [Paper].
• Suprosanna Shit, Johannes C. Paetzold, Anjany Sekuboyina, Ivan Ezhov, Alexander Unger, Andrey Zhylka, Josien PW Pluim, Ulrich Bauer, and Bjoern H. Menze. "clDice-a novel topology-preserving loss function for tubular structure segmentation." CVPR'2021. [Paper]
• Mingfei Cheng, Kaili Zhao, Xuhong Guo, Yajing Xu, and Jun Guo. "Joint topology-preserving and feature-refinement network for curvilinear structure segmentation." ICCV'2021. [Paper].
• Minh Ôn Vû Ngoc, Yizi Chen, Nicolas Boutry, Joseph Chazalon, Edwin Carlinet, Jonathan Fabrizio, Clément Mallet, and Thierry Géraud. "Introducing the Boundary-Aware loss for deep image segmentation." BMVC'2021. [Paper]
• Doruk Oner, Mateusz Koziński, Leonardo Citraro, Nathan C. Dadap, Alexandra G. Konings, and Pascal Fua. "Promoting connectivity of network-like structures by enforcing region separation." TPAMI'2021. [Paper]
• Xiaoling Hu. "Structure-aware image segmentation with homotopy warping." NeurIPS'2022. [Paper]
• Saumya Gupta, Xiaoling Hu, James Kaan, Michael Jin, Mutshipay Mpoy, Katherine Chung, Gagandeep Singh et al. "Learning topological interactions for multi-class medical image segmentation." ECCV'2022. [Paper]
• Tianyi Shi, Nicolas Boutry, Yongchao Xu, and Thierry Géraud. "Local intensity order transformation for robust curvilinear object segmentation." TIP'2022. [Paper]
• Nick Byrne, James R. Clough, Israel Valverde, Giovanni Montana, and Andrew P. King. "A persistent homology-based topological loss for CNN-based multiclass segmentation of CMR." TMI'2022. [Paper]
• Haotian Wang, Min Xian, and Aleksandar Vakanski. "Ta-net: Topology-aware network for gland segmentation." WACV'2022. [Paper]
• Nico Stucki, Johannes C. Paetzold, Suprosanna Shit, Bjoern Menze, and Ulrich Bauer. "Topologically faithful image segmentation via induced matching of persistence barcodes." ICML'2023. [Paper]
• Yaolei Qi, Yuting He, Xiaoming Qi, Yuan Zhang, and Guanyu Yang. "Dynamic snake convolution based on topological geometric constraints for tubular structure segmentation." ICCV'2023. [Paper]
• Hongliang He, Jun Wang, Pengxu Wei, Fan Xu, Xiangyang Ji, Chang Liu, and Jie Chen. "Toposeg: Topology-aware nuclear instance segmentation." CVPR'2023. [Paper]
• Ziyun Yang, and Sina Farsiu. "Directional connectivity-based segmentation of medical images." CVPR'2023. [Paper]
• Manxi Lin, Kilian Zepf, Anders Nymark Christensen, Zahra Bashir, Morten Bo Søndergaard Svendsen, Martin Tolsgaard, and Aasa Feragen. "Dtu-net: Learning topological similarity for curvilinear structure segmentation." IPMI'2023. [Paper]
• Liu Li, Qiang Ma, Cheng Ouyang, Zeju Li, Qingjie Meng, Weitong Zhang, Mengyun Qiao et al. "Robust segmentation via topology violation detection and feature synthesis." MICCAI'2023. [Paper]
• Ainkaran Santhirasekaram, Karen Pinto, Mathias Winkler, Andrea Rockall, and Ben Glocker. "A Sheaf Theoretic Perspective for Robust Prostate Segmentation." MICCAI'2023. [Paper]
• Doruk Oner, Adélie Garin, Mateusz Koziński, Kathryn Hess, and Pascal Fua. "Persistent homology with improved locality information for more effective delineation." TPAMI'2023. [Paper]
• Meilong Xu, Xiaoling Hu, Saumya Gupta, Shahira Abousamra, and Chao Chen. "TopoSemiSeg: Enforcing Topological Consistency for Semi-Supervised Segmentation of Histopathology Images." ECCV'2024. [Paper]
• Jiaxing Huang, Yanfeng Zhou, Yaoru Luo, Guole Liu, Heng Guo, and Ge Yang. "Representing Topological Self-Similarity Using Fractal Feature Maps for Accurate Segmentation of Tubular Structures." ECCV'24. [Paper]
• Qian Wu, Yufei Chen, Wei Liu, Xiaodong Yue, and Xiahai Zhuang. "Deep Closing: Enhancing Topological Connectivity in Medical Tubular Segmentation." TMI'2024 [Paper]
• Alexander H. Berger, Laurin Lux, Nico Stucki, Vincent Bürgin, Suprosanna Shit, Anna Banaszak, Daniel Rueckert, Ulrich Bauer, and Johannes C. Paetzold. "Topologically faithful multi-class segmentation in medical images." MICCAI'2024. [Paper]
• Pengcheng Shi, Jiesi Hu, Yanwu Yang, Zilve Gao, Wei Liu, and Ting Ma. "Centerline boundary dice loss for vascular segmentation." MICCAI'2024. [Paper]
• Liu Li, Hanchun Wang, Matthew Baugh, Qiang Ma, Weitong Zhang, Cheng Ouyang, Daniel Rueckert, and Bernhard Kainz. "Universal Topology Refinement for Medical Image Segmentation with Polynomial Feature Synthesis." MICCAI'2024. [Paper]
• Cesar Acebes, Abdel Hakim Moustafa, Oscar Camara, and Adrian Galdran. "The Centerline-Cross Entropy Loss for Vessel-Like Structure Segmentation: Better Topology Consistency Without Sacrificing Accuracy." MICCAI'2024. [Paper]
• Madeleine K. Wyburd, Nicola K. Dinsdale, Mark Jenkinson, and Ana IL Namburete. "Anatomically plausible segmentations: Explicitly preserving topology through prior deformations." MedIA'2024. [Paper]
• Nina I. Shamsi, Alec S. Xu, Lars A. Gjesteby, and Laura J. Brattain. "Improved Topological Preservation in 3D Axon Segmentation and Centerline Detection using Geometric Assessment-driven Topological Smoothing (GATS)." WACV'2024. [Paper]

Classification

• Fan Wang, Saarthak Kapse, Steven Liu, Prateek Prasanna, and Chao Chen. "TopoTxR: a topological biomarker for predicting treatment response in breast cancer." MICCAI'2021. [Paper]
• Yaopeng Peng, Hongxiao Wang, Milan Sonka, and Danny Z. Chen. "PHG-Net: Persistent Homology Guided Medical Image Classification." WACV'2024. [Paper]
• Fan Wang, Zhilin Zou, Nicole Sakla, Luke Partyka, Nil Rawal, Gagandeep Singh, Wei Zhao et al. "TopoTxR: A topology-guided deep convolutional network for breast parenchyma learning on DCE-MRIs." MedIA'2025. [Paper]

Detection

• Shahira Abousamra, David Belinsky, John Van Arnam, Felicia Allard, Eric Yee, Rajarsi Gupta, Tahsin Kurc, Dimitris Samaras, Joel Saltz, and Chao Chen. "Multi-class cell detection using spatial context representation." ICCV'2021. [Paper]

Registration

• Madeleine K. Wyburd, Nicola K. Dinsdale, Ana IL Namburete, and Mark Jenkinson. "TEDS-Net: enforcing diffeomorphisms in spatial transformers to guarantee topology preservation in segmentations." MICCAI'2021. [Paper]
• Yohai Reani, and Omer Bobrowski. "Cycle registration in persistent homology with applications in topological bootstrap." TPAMI'2022. [Paper]

Reconstruction

• Junyi Pan, Xiaoguang Han, Weikai Chen, Jiapeng Tang, and Kui Jia. "Deep mesh reconstruction from single rgb images via topology modification networks." ICCV'2019. [Paper]
• Dominik JE Waibel, Scott Atwell, Matthias Meier, Carsten Marr, and Bastian Rieck. "Capturing shape information with multi-scale topological loss terms for 3d reconstruction." MICCAI'2022. [Paper]
• Doruk Oner, Hussein Osman, Mateusz Koziński, and Pascal Fua. "Enforcing connectivity of 3D linear structures using their 2D projections." MICCAI'2022. [Paper]

Counting

• Shahira Abousamra, Minh Hoai, Dimitris Samaras, and Chao Chen. "Localization in the crowd with topological constraints." AAAI'2021. [Paper]

Uncertainty Estimation

• Xiaoling Hu, Dimitris Samaras, and Chao Chen. "Learning probabilistic topological representations using discrete morse theory." ICLR'2023. [Paper]
• Saumya Gupta, Yikai Zhang, Xiaoling Hu, Prateek Prasanna, and Chao Chen. "Topology-aware uncertainty for image segmentation." NeurIPS'2023. [Paper]

Generative Models

• Fan Wang, Huidong Liu, Dimitris Samaras, and Chao Chen. "Topogan: A topology-aware generative adversarial network." ECCV'2020. [Paper]
• Shahira Abousamra, Rajarsi Gupta, Tahsin Kurc, Dimitris Samaras, Joel Saltz, and Chao Chen. "Topology-guided multi-class cell context generation for digital pathology." CVPR'2023. [Paper]
• Meilong Xu, Saumya Gupta, Xiaoling Hu, Chen Li, Shahira Abousamra, Dimitris Samaras, Prateek Prasanna, and Chao Chen. "TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model." arXiv'2024. [Paper]

Other Topics

• Mathieu Carriere, and Andrew Blumberg. "Multiparameter persistence image for topological machine learning." NeurIPS'2020. [Paper]
• Fan Wang, Hubert Wagner, and Chao Chen. "GPU Computation of the Euler Characteristic Curve for Imaging Data." SoCG'2022. [Paper]
• Theodore Papamarkou, Tolga Birdal, Michael Bronstein, Gunnar Carlsson, Justin Curry, Yue Gao, Mustafa Hajij et al. "Position: Topological Deep Learning is the New Frontier for Relational Learning." arXiv'2024. [Paper]
• Chia-Chia Chen, and Chi-Han Peng. "Topology-Preserving Downsampling of Binary Images." ECCV'2024. [Paper]
• Ilya Trofimov, Daria Voronkova, Eduard Tulchinskii, Evgeny Burnaev, and Serguei Barannikov. "Scalar Function Topology Divergence: Comparing Topology of 3D Objects." ECCV'2024. [Paper]

Maintainers - Xiaoling Hu