A Framework For Evaluating Visual SLAM. - Tobias Pietzsch; Jan Funke (BMVC, 2009)

Multi-Hypothesis CRF-Segmentation of Neural Tissue in Anisotropic EM Volumes - Jan Funke; Björn Andres; Fred A. Hamprecht; Albert Cardona; Matthew Cook 001 (CoRR, 2011)

Efficient automatic 3D-reconstruction of branching neurons from EM data. - Jan Funke; Björn Andres; Fred A. Hamprecht; Albert Cardona; Matthew Cook 001 (CVPR, 2012)

Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine. - Florian Jug; Tobias Pietzsch; Dagmar Kainmüller; Jan Funke; Matthias Kaiser; Erik van Nimwegen; Carsten Rother; Gene Myers (BAMBI, 2014)

Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes. - Jan Funke; Julien N. P. Martel; Stephan Gerhard; Björn Andres; Dan C. Ciresan; Alessandro Giusti; Luca Maria Gambardella; Jürgen Schmidhuber; Hanspeter Pfister; Albert Cardona; Matthew Cook 001 (MICCAI (1), 2014)

Automatic Neuron Reconstruction from Anisotropic Electron Microscopy Volumes. - Jan Funke (2014)

Learning to Segment: Training Hierarchical Segmentation under a Topological Loss. - Jan Funke; Fred A. Hamprecht; Chong Zhang 001 (MICCAI (3), 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)

A Tolerant Edit Distance for Evaluation and Training of Electron Microscopy Reconstruction Algorithms. - Jan Funke; Jonas Klein; Albert Cardona; Matthew Cook 001 (CoRR, 2015)

Accurate and Linear Time Pose Estimation from Points and Lines. - Alexander Vakhitov; Jan Funke; Francesc Moreno-Noguer (ECCV (7), 2016)

Tracking of microtubules in anisotropic volumes of neural tissue. - Julia M. Buhmann; Stephan Gerhard; Matthew Cook 001; Jan Funke (ISBI, 2016)

Structured learning of assignment models for neuron reconstruction to minimize topological errors. - Jan Funke; Jonas Klein; Francesc Moreno-Noguer; Albert Cardona; Matthew Cook 001 (ISBI, 2016)

Efficient convolutional neural networks for pixelwise classification on heterogeneous hardware systems. - Fabian Tschopp; Julien N. P. Martel; Srinivas C. Turaga; Matthew Cook 001; Jan Funke (ISBI, 2016)

The Candidate Multi-Cut for Cell Segmentation. - Jan Funke; Chong Zhang 001; Tobias Pietzsch; Stephan Saalfeld (CoRR, 2017)

A Deep Structured Learning Approach Towards Automating Connectome Reconstruction from 3D Electron Micrographs. - Jan Funke; Fabian Tschopp; William Grisaitis; Arlo Sheridan; Chandan Singh; Stephan Saalfeld; Srinivas C. Turaga (CoRR, 2017)

A Benchmark for Epithelial Cell Tracking. - Jan Funke; Lisa Mais; Andrew Champion; Natalie Dye; Dagmar Kainmueller (ECCV Workshops (6), 2018)

The candidate multi-cut for cell segmentation. - Jan Funke; Chong Zhang 001; Tobias Pietzsch; Miguel Ángel González Ballester; Stephan Saalfeld (ISBI, 2018)

Synaptic Partner Prediction from Point Annotations in Insect Brains. - Julia M. Buhmann; Renate Krause; Rodrigo Ceballos Lentini; Nils Eckstein; Matthew Cook 001; Srinivas C. Turaga; Jan Funke (MICCAI (2), 2018)

Synaptic Cleft Segmentation in Non-isotropic Volume Electron Microscopy of the Complete Drosophila Brain. - Larissa Heinrich; Jan Funke; Constantin Pape; Juan Nunez-Iglesias; Stephan Saalfeld (MICCAI (2), 2018)

Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction. - Jan Funke; Fabian Tschopp; William Grisaitis; Arlo Sheridan; Chandan Singh; Stephan Saalfeld; Srinivas C. Turaga (IEEE Trans. Pattern Anal. Mach. Intell., 2019)

Inpainting Networks Learn to Separate Cells in Microscopy Images. - Steffen Wolf 001; Fred A. Hamprecht; Jan Funke (BMVC, 2020)

Microtubule Tracking in Electron Microscopy Volumes. - Nils Eckstein; Julia M. Buhmann; Matthew Cook 001; Jan Funke (MICCAI (5), 2020)

Instance Separation Emerges from Inpainting. - Steffen Wolf 001; Fred A. Hamprecht; Jan Funke (CoRR, 2020)

How Shift Equivariance Impacts Metric Learning for Instance Segmentation. - Josef Lorenz Rumberger; Xiaoyan Yu; Peter Hirsch 001; Melanie Dohmen; Vanessa Emanuela Guarino; Ashkan Mokarian; Lisa Mais; Jan Funke; Dagmar Kainmueller (ICCV, 2021)

Discriminative Attribution from Counterfactuals. - Nils Eckstein; Alexander S. Bates; Gregory S. X. E. Jefferis; Jan Funke (CoRR, 2021)

Discriminative Attribution from Paired Images. - Nils Eckstein; Habib Bukhari; Alexander S. Bates; Gregory S. X. E. Jefferis; Jan Funke (ECCV Workshops (4), 2022)

Tracking by Weakly-Supervised Learning and Graph Optimization for Whole-Embryo C. elegans lineages. - Peter Hirsch 001; Caroline Malin-Mayor; Anthony Santella; Stephan Preibisch; Dagmar Kainmueller; Jan Funke (MICCAI (4), 2022)

Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images. - Steffen Wolf 001; Manan Lalit; Katie McDole; Jan Funke (ICCV, 2023)

Unpaired Image Enhancement for Neurite Segmentation in x-ray Tomography. - Jeff L. Rhoades; Arlo Sheridan; Mukul Narwani; Brian Reicher; Mark Larson; Shuhan Xie; Tri Nguyen; Aaron T. Kuan; Alexandra Pacureanu; Wei-Chung Allen Lee 001; Jan Funke (ISBI, 2023)

Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images. - Steffen Wolf 001; Manan Lalit; Henry Westmacott; Katie McDole; Jan Funke (CoRR, 2023)

Model Based Inference of Synaptic Plasticity Rules. - Yash Mehta; Danil Tyulmankov; Adithya Rajagopalan; Glenn Turner; James Fitzgerald; Jan Funke (NeurIPS, 2024)

DaCapo: a modular deep learning framework for scalable 3D image segmentation. - William Patton; Jeff L. Rhoades; Marwan Zouinkhi; David G. Ackerman; Caroline Malin-Mayor; Diane Adjavon; Larissa Heinrich; Davis Bennett; Yurii Zubov; CellMap Project Team; Aubrey V. Weigel; Jan Funke (CoRR, 2024)