Publications

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2015
Kreshuk, A, Walecki, R, Köthe, U, Gierthmühlen, M, Plachta, D, Genoud, C, Haastert-Talini, K and Hamprecht, F A (2015). Automated Tracing of Myelinated Axons and Detection of the Nodes of Ranvier in Serial Images of Peripheral Nerves. Journal of Microscopy. 259 (2) 143-154
Kandemir, M and Hamprecht, F A (2015). Cell event detection in phase-contrast microscopy sequences from few annotations. MICCAI. Proceedings. Springer. LNCS 9351 316-323PDF icon Technical Report (564.69 KB)
Kappes, J H, Andres, B, Hamprecht, F A, Schnörr, C, Nowozin, S, Batra, D, Kim, S, Kausler, B X, Kröger, T, Lellmann, J, Komodakis, N, Savchynskyy, B and Rother, C (2015). A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems. International Journal of Computer Vision. 1-30PDF icon Technical Report (1.5 MB)
Kappes, J H, Andres, B, Hamprecht, F A, Schnörr, C, Nowozin, S, Batra, D, Kim, S, Kausler, B X, Kröger, T, Lellmann, J, Komodakis, N, Savchynskyy, B and Rother, C (2015). A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems. Int.~J.~Comp.~VisionPDF icon Technical Report (5.12 MB)
Kandemir, M and Hamprecht, F A (2015). The Deep Feed-Forward Gaussian Process: An Effective Generalization to Covariance Priors. NIPS. Proceedings. 44 145-159PDF icon Supplementary Material (223.39 KB)PDF icon Technical Report (2.58 MB)
Beier, T, Hamprecht, F A and Kappes, J H (2015). Fusion Moves for Correlation Clustering. CVPR. Proceedings. 3507-3516PDF icon Technical Report (1.19 MB)
Schiegg, M, Hanslovsky, P, Haubold, C, Köthe, U, Hufnagel, L and Hamprecht, F A (2015). Graphical Model for Joint Segmentation and Tracking of Multiple Dividing Cell. Bioinformatics. 31 948-956. http://bioinformatics.oxfordjournals.org/content/early/2014/11/17/bioinformatics.btu764.full.pdf?keytype=ref&ijkey=mTXWsiFrci7R8tcPDF icon Technical Report (534.29 KB)
Krasowski, N, Beier, T, Knott, G W, Köthe, U, Hamprecht, F A and Kreshuk, A (2015). Improving 3D EM Data Segmentation by Joint Optimization over Boundary Evidence and Biological Priors. 12th {IEEE} International Symposium on Biomedical Imaging, {ISBI} 2015, Brooklyn, NY, USA, April 16-19, 2015. 536-539PDF icon Technical Report (2.25 MB)
Funke, J, Hamprecht, F A and Zhang, C (2015). Learning to Segment: Training Hierarchical Segmentation under a Topological Loss. MICCAI. Proceedings, Part III. Springer. 9351 268-275PDF icon Technical Report (2.92 MB)
Schiegg, M, Heuer, B, Haubold, C, Wolf, S, Köthe, U and Hamprecht, F A (2015). Proof-reading Guidance in Cell Tracking by Sampling from Tracking-by-assignment Models. ISBI. Proceedings. 394-398PDF icon Technical Report (648.55 KB)
Cali, C, Baghabra, J, Boges, D J, Holst, G R, Kreshuk, A, Hamprecht, F A, Srinivasan, M, Lehväslaiho, H and Magistretti, P J (2015). Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. Journal of Comparative Neurology. 524 23-38
Kreshuk, A, Funke, J, Cardona, A and Hamprecht, F A (2015). Who is talking to whom: synaptic partner detection in anisotropic volumes of insect brain. MICCAI. Proceedings. Springer. LNCS 9349 661-668PDF icon Technical Report (2.14 MB)
2014
Lou, X, Schiegg, M and Hamprecht, F A (2014). Active Structured Learning for Cell Tracking: Algorithm, Framework and Usability. IEEE Transactions on Medical Imaging. 33 (4) 849-860PDF icon Technical Report (6.84 MB)
Kröger, T, Kappes, J H, Beier, T, Köthe, U and Hamprecht, F A (2014). Asymmetric Cuts: Joint Image Labeling and Partitioning. Pattern Recognition - 36th German Conference, {GCPR} 2014, Münster, Germany, September 2-5, 2014, Proceedings. http://dx.doi.org/10.1007/978-3-319-11752-2_16PDF icon Technical Report (3.46 MB)
Tek, B F, Kröger, T, Mikula, S and Hamprecht, F A (2014). Automated Cell Nucleus Detection for Large-Volume Electron Microscopy of Neural Tissue. ISBI. Proceedings. 69-72PDF icon Technical Report (533.92 KB)
Kreshuk, A, Köthe, U, Pax, E, Bock, D D and Hamprecht, F A (2014). Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks. PLoS ONE. 9 2PDF icon Technical Report (16.66 MB)
Zhang, C, Yarkony, J and Hamprecht, F A (2014). Cell detection and segmentation using correlation clustering. MICCAI. Proceedings. Springer. 9-16PDF icon Technical Report (8.06 MB)
Kappes, J H, Andres, B, Hamprecht, F A, Schnörr, C, Nowozin, S, Batra, D, Kim, S, Kausler, B X, Kröger, T, Lellmann, J, Komodakis, N, Savchynskyy, B and Rother, C (2014). A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems. CoRR. abs/1404.0533. http://hci.iwr.uni-heidelberg.de/opengm2/PDF icon Technical Report (3.32 MB)
Kappes, J H, Andres, B, Hamprecht, F A, Schnörr, C, Nowozin, S, Batra, D, Kim, S, Kausler, B X, Kröger, T, Lellmann, J, Komodakis, N, Savchynskyy, B and Rother, C (2014). A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems. CoRR. http://arxiv.org/abs/1404.0533
Kandemir, M and Hamprecht, F A (2014). Computer-aided diagnosis from weak supervision: A benchmarking study. Computerized Medical Imaging and Graphics. 42 44-50PDF icon Technical Report (4.28 MB)
Beier, T, Kröger, T, Kappes, J H, Köthe, U and Hamprecht, F A (2014). Cut, Glue and Cut: A Fast, Approximate Solver for Multicut Partitioning. 2014 {IEEE} Conference on Computer Vision and Pattern Recognition, {CVPR} 2014, Columbus, OH, USA, June 23-28, 2014. http://dx.doi.org/10.1109/CVPR.2014.17PDF icon Technical Report (10.06 MB)
Decker, C and Hamprecht, F A (2014). Detecting individual body parts improves mouse behavior classification. Workshop on visual observation and analysis of Vertebrate And Insect Behavior (VAIB), 22nd International Conference on Pattern Recognition (ICPR). ProceedingsPDF icon Technical Report (1.48 MB)
Kandemir, M, Feuchtinger, A, Walch, A and Hamprecht, F A (2014). Digital Pathology: Multiple instance learning can detect Barrett'scancer. ISBI. Proceedings. 1348-1351PDF icon Technical Report (2.86 MB)
Kandemir, M, Zhang, C and Hamprecht, F A (2014). Empowering multiple instance histopathology cancer diagnosis by cell graphs. MICCAI. Proceedings. Springer. 8674 228-235PDF icon Technical Report (1.76 MB)
Kandemir, M, Rubio, J C, Schmidt, U, Welbl, J, Ommer, B and Hamprecht, F A (2014). Event Detection by Feature Unpredictability in Phase-Contrast Videos of Cell Cultures. MICCAI. Proceedings. Springer. 154-161PDF icon Paper (2 MB)
Lindner, R, Lou, X, Reinstein, J, Shoeman, R L, Hamprecht, F A and Winkler, A (2014). Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation. Journal of The American Society for Mass Spectrometry. 25 1018-1028PDF icon Technical Report (2.1 MB)
Kleesiek, J, Biller, A, Urban, G, Köthe, U, Bendszus, M and Hamprecht, F A (2014). ilastik for Multi-modal Brain Tumor Segmentation. MICCAI BraTS (Brain Tumor Segmentation) Challenge. Proceedings, 3rdplace. 12-17PDF icon Technical Report (405.91 KB)
Kandemir, M and Hamprecht, F A (2014). Instance Label Prediction by Dirichlet Process Multiple Instance Learning. UAI. ProceedingsPDF icon Technical Report (4.26 MB)

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