All Publications


Pape, C, Remme, R, Wolny, A, Olberg, S, Wolf, S, Cerrone, L, Cortese, M, Klaus, S, Lucic, B, Ullrich, S, Anders-Össwein, M, Wolf, S, Cerikan, B, Neufeldt, C J, Ganter, M, Schnitzler, P, Merle, U, Lusic, M, Boulant, S, Stanifer, M, Bartenschlager, R, Hamprecht, F A, Kreshuk, A, Tischer, C, Kräusslich, H - G, Müller, B and Laketa, V (2020). Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera. BioEssays, in press
Bailoni, A, Pape, C, Wolf, S, Kreshuk, A and Hamprecht, F A (2020). Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks. GCPR, accepted. arXiv
Wolf, S, Hamprecht, F A and Funke, J (2020). Inpainting Networks Learn to Separate Cells in Microscopy Images. BMCV, in pressPDF icon Technical Report (357.23 KB)
Wolny, A, Cerrone, L, Vijayan, A, Tofanelli, R, A Barro, V, Louveaux, M, Wenzl, C, Steigleder, S, Pape, C, Bailoni, A, Duran-Nebreda, S, Bassel, G W, Lohmann, J U, Hamprecht, F A, Schneitz, K, Maizel, A and Kreshuk, A (2020). Accurate and versatile 3D segmentation of plant tissues at cellular resolution. eLife, in press
Wolf, S, Li, Y, Pape, C, Bailoni, A, Kreshuk, A and Hamprecht, F A (2020). The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation. ECCV. Proceedings. 208-224
Wolf, S (2020). Machine Learning for Instance Segmentation. Heidelberg University
Wolf, S, Bailoni, A, Pape, C, Rahaman, N, Kreshuk, A, Köthe, U and Hamprecht, F A (2020). The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning. IEEE Transactions on Pattern Analysis and Machine IntelligencePDF icon Technical Report (2.58 MB)
Bollweg, S, Haußmann, M, Kasieczka, G, Luchmann, M, Plehn, T and Thompson, J (2020). Deep-Learning Jets with Uncertainties and More. SciPost Phys. 8. icon Technical Report (1.65 MB)


Haußmann, M, Hamprecht, F A and Kandemir, M (2019). Sampling-Free Variational Inference of Bayesian Neural Networks by Variance Backpropagation. UAI. ProceedingsPDF icon Technical Report (1.04 MB)
Kirschbaum, E, Haußmann, M, Wolf, S, Sonntag, H, Schneider, J, Elzoheiry, S, Kann, O, Durstewitz, D and Hamprecht, F A (2019). LeMoNADe: Learned Motif and Neuronal Assembly Detection in calcium imaging videos. ICLR. Proceedings
Bendinger, A L, Debus, C, Glowa, C, Karger, C P, Peter, J and Storath, M (2019). Bolus arrival time estimation in dynamic contrast-enhanced magnetic resonance imaging of small animals based on spline models, in press. Physics in Medicine and Biology. 64
Cerrone, L, Zeilmann, A and Hamprecht, F A (2019). End-to-End Learned Random Walker for Seeded Image Segmentation. CVPR. Proceedings. 12559-12568
Li, J (2019). Robust Single Object Tracking Via Fully Convolutional Siamese Networks. Heidelberg University
Li, Y (2019). Semantic Instance Segmentation With The Multiway Mutex Watershed. Heidelberg University
Bengio, Y, Deleu, T, Rahaman, N, Ke, R, Lachapelle, S, Bilaniuk, O, Goyal, A and Pal, C (2019). A Meta-Transfer Objective for Learning to Disentangle Causal Mechanisms. arXiv preprint arXiv:1901.10912PDF icon Technical Report (871.59 KB)
Haußmann, M, Hamprecht, F A and Kandemir, M (2019). Deep Active Learning with Adaptive Acquisition. IJCAI. Proceedings. 2470-2476PDF icon Technical Report (137.6 KB)
Haußmann, M, Gerwinn, S and Kandemir, M (2019). Bayesian Prior Networks with PAC Training. arXiv preprint arXiv:1906.00816
Hehn, T M, Kooij, J F P and Hamprecht, F A (2019). End-to-End Learning of Decision Trees and Forests. International Journal of Computer Vision. 128 997-1011
Berg, S, Kutra, D, Kroeger, T, Straehle, C N, Kausler, B X, Haubold, C, Schiegg, M, Ales, J, Beier, T, Rudy, M, Eren, K, Cervantes, J I, Xu, B, Beuttenmüller, F, Wolny, A, Zhang, C, Köthe, U, Hamprecht, F A and Kreshuk, A (2019). ilastik: interactive machine learning for (bio)image analysis. Nature Methods. 16 1226-1232
Kiefer, L, Storath, M and Weinmann, A (2019). An efficient algorithm for the piecewise affine-linear Mumford-Shah model based on a Taylor jet splitting. IEEE Transactions on Image Processing. 29PDF icon Technical Report (2.04 MB)
Storath, M, Kiefer, L and Weinmann, A (2019). Smoothing for signals with discontinuities using higher order Mumford-Shah models. Numerische Mathematik. 143(2) 423-460PDF icon Technical Report (1.09 MB)
Esposito, M, Hennersperger, C, Göbl, R, Demaret, L, Storath, M, Navab, N, Baust, M and Weinmann, A (2019). Total variation regularization of pose signals with an application to 3D freehand ultrasound. IEEE Transactions on Medical Imaging. 38(10) 2245-2258
E Sanmartin, F, Damrich, S and Hamprecht, F A (2019). Probabilistic Watershed: Sampling all spanning forests for seeded segmentation and semi-supervised learning. Advances in Neural Information Processing Systems
Peter, S (2019). Machine learning under test-time budget constraints. Heidelberg University
Xiao, S (2019). Tracking Dividing Cells Using Spatio-Temporal Embeddings. Heidelberg
Ravindran, A (2019). Novel Deep Learning-Based Instance Segmentation Using Mutex Watershed For Microscopy Cell Images. Heidelberg University
Hanslovsky, P (2019). Isotropic Reconstruction of Neural Morphology from Large Non-Isotropic 3D Electron MIcroscopy. Heidelberg University
Fita, E (2019). Semi-Supervised Distance-Based Segmentation. Heidelberg University
Remme, R (2019). Instance Segmentation Via Associative Pixel Embeddings. Heidelberg University
Snajder, R (2019). Pipeline Für Die Automatisierte Objektsegmentierung Von 3D Lightshet Mikroskopiebildern. Heidelberg University
Großkinsky, (2019). Synaptic Cleft Prediction On Electron Microsope Images. Heidelberg University
Pandey, N (2019). Weakly Supervised Semantic Segmentation. Heidelberg University
Kirschbaum, E (2019). Novel Machine Learning Approaches for Neurophysiological Data Analysis. Heidelberg University


Draxler, F, Veschgini, K, Salmhofer, M and Hamprecht, F A (2018). Essentially No Barriers in Neural Network Energy Landscape. ICML. Proceedings. 80 1308--1317PDF icon Technical Report (685.93 KB)
Wolf, S, Pape, C, Bailoni, A, Rahaman, N, Kreshuk, A, Köthe, U and Hamprecht, F A (2018). The Mutex Watershed: Efficient, Parameter-Free Image Partitioning. ECCV. Proceedings. Springer. 571-587
Fortun, D, Storath, M, Rickert, D, Weinmann, A and Unser, M (2018). Fast Piecewise-Affine Motion Estimation Without Segmentation. IEEE Transactions on Image Processing. 27 5612 - 5624
Erb, W, Weinmann, A, Ahlborg, M, Brandt, C, Bringout, G, Buzug, T M, Frikel, J, Kaethner, C, Knopp, T, März, T, Möddel, M, Storath, M and Weber, A (2018). Mathematical Analysis of the 1D Model and Reconstruction Schemes for Magnetic Particle Imaging. Inverse Problems. 34
Bredies, K, Holler, M, Storath, M and Weinmann, A (2018). Total Generalized Variation for Manifold-valued Data. SIAM Journal on Imaging Sciences. 11 1785 - 1848
Schimmel, F (2018). Learnability Of Approximated Graph Cut Segmentation. Heidelberg University
Kawetzki, D (2018). Semantic Segmentation Of Urban Scenes Using Deep Learning. Heidelberg University