Developments in ROOT I/O and trees - Rene Brun; Philippe Canal; Mario Frank; Anna Kreshuk; S. Linev; Paul Russo; Fons Rademakers (CoRR, 2009)

ROOT - A C++ framework for petabyte data storage, statistical analysis and visualization. - Ilka Antcheva; Maarten Ballintijn; Bertrand Bellenot; Marek Biskup; Rene Brun; Nenad Buncic; Philippe Canal; Diego Casadei; Olivier Couet; Valery Fine; Leandro Franco; Gerardo Ganis; et al. (Comput. Phys. Commun., 2009)

Automated segmentation of synapses in 3D EM data. - Anna Kreshuk; Christoph N. Straehle; Christoph Sommer 002; Ullrich Köthe; Graham Knott; Fred A. Hamprecht (ISBI, 2011)

ROOT - A C++ framework for petabyte data storage, statistical analysis and visualization. - Ilka Antcheva; Maarten Ballintijn; Bertrand Bellenot; Marek Biskup; Rene Brun; Nenad Buncic; Philippe Canal; Diego Casadei; Olivier Couet; Valery Fine; Leandro Franco; Gerardo Ganis; et al. (Comput. Phys. Commun., 2011)

Automated Analysis of Biomedical Data from Low to High Resolution - Anna Kreshuk (2012)

Improving 3D EM data segmentation by joint optimization over boundary evidence and biological priors. - Nikola Krasowski; Thorsten Beier; Graham W. Knott; Ullrich Köthe; Fred A. Hamprecht; Anna Kreshuk (ISBI, 2015)

Who Is Talking to Whom: Synaptic Partner Detection in Anisotropic Volumes of Insect Brain. - Anna Kreshuk; Jan Funke; Albert Cardona; Fred A. Hamprecht (MICCAI (1), 2015)

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization. - Ilka Antcheva; Maarten Ballintijn; Bertrand Bellenot; Marek Biskup; Rene Brun; Nenad Buncic; Philippe Canal; Diego Casadei; Olivier Couet; Valery Fine; Leandro Franco; Gerardo Ganis; et al. (CoRR, 2015)

Solving Large Multicut Problems for Connectomics via Domain Decomposition. - Constantin Pape; Thorsten Beier; Peter Li; Viren Jain; Davi D. Bock; Anna Kreshuk (ICCV Workshops, 2017)

The Mutex Watershed: Efficient, Parameter-Free Image Partitioning. - Steffen Wolf 001; Constantin Pape; Alberto Bailoni; Nasim Rahaman; Anna Kreshuk; Ullrich Köthe; Fred A. Hamprecht (ECCV (4), 2018)

Neuron Segmentation With High-Level Biological Priors. - Nikola Krasowski; Thorsten Beier; Graham Knott; Ullrich Köthe; Fred A. Hamprecht; Anna Kreshuk (IEEE Trans. Medical Imaging, 2018)

Domain Adaptive Segmentation In Volume Electron Microscopy Imaging. - Joris Roels; Julian Hennies; Yvan Saeys; Wilfried Philips; Anna Kreshuk (ISBI, 2019)

Synthetic Patches, Real Images: Screening for Centrosome Aberrations in EM Images of Human Cancer Cells. - Artem Lukoyanov; Isabella Haberbosch; Constantin Pape; Alwin Krämer; Yannick Schwab; Anna Kreshuk (MICCAI (1), 2019)

The Mutex Watershed and its Objective: Efficient, Parameter-Free Image Partitioning. - Steffen Wolf 001; Alberto Bailoni; Constantin Pape; Nasim Rahaman; Anna Kreshuk; Ullrich Köthe; Fred A. Hamprecht (CoRR, 2019)

Leveraging Domain Knowledge to improve EM image segmentation with Lifted Multicuts. - Constantin Pape; Alex Matskevych; Julian Hennies; Anna Kreshuk (CoRR, 2019)

A Generalized Framework for Agglomerative Clustering of Signed Graphs applied to Instance Segmentation. - Alberto Bailoni; Constantin Pape; Steffen Wolf 001; Thorsten Beier; Anna Kreshuk; Fred A. Hamprecht (CoRR, 2019)

Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts. - Constantin Pape; Alex Matskevych; Adrian Wolny; Julian Hennies; Giulia Mizzon; Marion Louveaux; Jacob Musser; Alexis Maizel; Detlev Arendt; Anna Kreshuk (Frontiers Comput. Sci., 2019)

QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. - Sharon C. Yates; Nicolaas E. Groeneboom; Christopher Coello; Stefan F. Lichtenthaler; Peer-Hendrik Kuhn; Hans-Ulrich Demuth; Maike Hartlage-Rübsamen; Steffen Roßner; Trygve B. Leergaard; Anna Kreshuk; Maja A. Puchades; Jan G. Bjaalie (Frontiers Neuroinformatics, 2019)

Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks. - Alberto Bailoni; Constantin Pape; Steffen Wolf 001; Anna Kreshuk; Fred A. Hamprecht (GCPR, 2020)

The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation. - Steffen Wolf 001; Yuyan Li; Constantin Pape; Alberto Bailoni; Anna Kreshuk; Fred A. Hamprecht (ECCV (6), 2020)

Stateless actor-critic for instance segmentation with high-level priors. - Paul Hilt; Edgar Kaziakhmedov; Sourabh Bhide; Maria Leptin; Constantin Pape; Anna Kreshuk (CoRR, 2021)

Developing open-source software for bioimage analysis: opportunities and challenges. - Florian Levet; Anne E. Carpenter; Kevin W. Eliceiri; Anna Kreshuk; Peter Bankhead; Robert Haase 001 (F1000Research, 2021)

The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning. - Steffen Wolf 001; Alberto Bailoni; Constantin Pape; Nasim Rahaman; Anna Kreshuk; Ullrich Köthe; Fred A. Hamprecht (IEEE Trans. Pattern Anal. Mach. Intell., 2021)

GASP, a generalized framework for agglomerative clustering of signed graphs and its application to Instance Segmentation. - Alberto Bailoni; Constantin Pape; Nathan Hütsch; Steffen Wolf 001; Thorsten Beier; Anna Kreshuk; Fred A. Hamprecht (CVPR, 2022)

Sparse Object-level Supervision for Instance Segmentation with Pixel Embeddings. - Adrian Wolny; Qin Yu 005; Constantin Pape; Anna Kreshuk (CVPR, 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

From Shallow to Deep: Exploiting Feature-Based Classifiers for Domain Adaptation in Semantic Segmentation. - Alex Matskevych; Adrian Wolny; Constantin Pape; Anna Kreshuk (Frontiers Comput. Sci., 2022)

Reinforcement learning for instance segmentation with high-level priors. - Paul Hilt; Maedeh Zarvandi; Edgar Kaziakhmedov; Sourabh Bhide; Maria Leptin; Constantin Pape; Anna Kreshuk (ICCV (Workshops), 2023)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

Spherical harmonics texture extraction for versatile analysis of biological objects. - Oane Gros; Josiah B. Passmore; Noa O. Borst; Dominik Kutra; Wilco Nijenhuis; Timothy Fuqua; Lukas C. Kapitein; Justin M. Crocker; Anna Kreshuk; Simone Köhler (PLoS Comput. Biol., 2025)

Ranking pre-trained segmentation models for zero-shot transferability. - Joshua Talks; Anna Kreshuk (CoRR, 2025)

Tiling artifacts and trade-offs of feature normalization in the segmentation of large biological images. - Elena Buglakova; Anwai Archit; Edoardo D'Imprima; Julia Mahamid; Constantin Pape; Anna Kreshuk (CoRR, 2025)