All Publications

2012
Kausler, B X, Schiegg, M, Andres, B, Lindner, M, Köthe, U, Leitte, H, Wittbrodt, J, Hufnagel, L and Hamprecht, F A (2012). A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness. ECCV 2012. Proceedings. 7574 144-157 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (809.07 KB)
Lou, X, Fiaschi, L, Köthe, U and Hamprecht, F A (2012). Quality Classification of Microscopic Imagery with Weakly Supervised Learning. MICCAI-MLMI. Proceedings. 176-183 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (4.15 MB)
Lou, X and Hamprecht, F A (2012). Structured Learning from Partial Annotations. ICML 2012. Proceedings. http://icml.cc/discuss/2012/753.html Google Scholar BibTeX RTF EndNote XML Technical Report (843.45 KB)
Röder, J, Kunzmann, K, Nadler, B and Hamprecht, F A (2012). Active Learning with Distributional Estimates. UAI 2012. Proceedings. 715-725 Google Scholar BibTeX RTF EndNote XML Technical Report (267.67 KB)
Renard, B Y, Xu, B, Kirchner, M, Zickmann, F, Winter, D, Korten, S, Brattig, N, Tzur, A, Hamprecht, F A and Steen, H (2012). Overcoming species boundaries in peptide identification with BICEPS. Molecular and Cellular Proteomics. 11 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (444.6 KB)
Sommer, C, Fiaschi, L, Hamprecht, F A and Gerlich, D (2012). Learning-based Mitotic Cell Detection in Histopathological Images. ICPR 2012. Proceedings. 2306-2309 Google Scholar BibTeX RTF EndNote XML Technical Report (1.96 MB)
Straehle, C N, Köthe, U, Briggman, K, Denk, W and Hamprecht, F A (2012). Seeded watershed cut uncertainty estimators for guided interactive segmentation. CVPR 2012. Proceedings. 765 - 772 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (2.84 MB)
Zechmann, C M, Menze, B H, Kelm, B Michael, Zamecnik, P, Ikinger, U, Waldherr, R, Delorme, S, Hamprecht, F A and Bachert, P (2012). Automated vs. manual pattern recognition of 3D 1H MRSI data of patients with prostate cancer. Academic Radiology. 19, 6 675-684 DOI Google Scholar BibTeX RTF EndNote XML
Kreshuk, A (2012). Automated Analysis of Biomedical Data from Low to High Resolution. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Lou, X and Hamprecht, F A (2012). Learning to Segment Dense Cell Nuclei with Shape Prior. CVPR 2012. Proceedings. 1012-1018 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (2.66 MB)

2011
Andres, B (2011). Automated Segmentation of Large 3D Images of Nervous Systems Using a Higher-order Graphical Model. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Andres, B, Kappes, J H, Beier, T, Köthe, U and Hamprecht, F A (2011). Probabilistic Image Segmentation with Closedness Constraints. ICCV, Proceedings. 2611 - 2618 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (8.18 MB)
Frank, M and Hamprecht, F A (2011). Image-Based Supervision of a Periodically Working Machine. Pattern Analysis and Applications. 1-10 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (466.61 KB)
Hanselmann, M, Voss, B, Renard, B Y, Lindner, M, Köthe, U, Kirchner, M and Hamprecht, F A (2011). SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. Bioinformatics. 27 (7) 987-993 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (2.2 MB)
Kappes, J H, Speth, M, Andres, B, Reinelt, G and Schnörr, C (2011). Globally Optimal Image Partitioning by Multicuts. EMMCVPR. Springer. 31-44 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (7.3 MB)
Kaster, F O (2011). Image Analysis for the Life Sciences - Computer-assisted Tumor Diagnostics and Digital Embryomics. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Kaster, F O, Weber, M - A and Hamprecht, F A (2011). Comparative Validation of Graphical Models for Learning Tumor Segmentations from Noisy Manual Annotations. LNCS. Springer, Heidelberg. LNCS 6533 74-85 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (544.56 KB)
Kaster, F O, Merkel, B, Nix, O and Hamprecht, F A (2011). An object-oriented library for systematic training and comparison of classifiers for computer-assisted tumor diagnosis from MRSI measurements. Computer Science - Research and Development. 26 65-85 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (808.16 KB)
Kelm, B Michael, Kaster, F O, Henning, A, Weber, M - A, Bachert, P, Bösinger, P, Hamprecht, F A and Menze, B H (2011). Using Spatial Prior Knowledge in the Spectral Fitting of Magnetic Resonance Spectroscopic Images. NMR in Biomedicine. 25(1) 1-13 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (1.94 MB)
Kreshuk, A, Straehle, C N, Sommer, C, Köthe, U, Cantoni, M, Knott, G W and Hamprecht, F A (2011). Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images. PLoS ONE. 6 (10) DOI Google Scholar BibTeX RTF EndNote XML Technical Report (290.48 KB)
Lindner, M (2011). A Machine Learning Approach To Improve Digital Embryo Analysis. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Lou, X (2011). Biomedical Data Analysis with Prior Knowledge: Modeling and Learning. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Lou, X and Hamprecht, F A (2011). Structured Learning for Cell Tracking. NIPS 2011. Proceedings. 1296-1304 Google Scholar BibTeX RTF EndNote XML Technical Report (1.41 MB)
Lou, X, Kaster, F O, Lindner, M, Kausler, B X, Köthe, U, Höckendorf, B, Wittbrodt, J, Jänicke, H and Hamprecht, F A (2011). DELTR: Digital Embryo Lineage Tree Reconstructor. Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings. 1557-1560 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (1.44 MB)
Menze, B H, Kelm, B Michael, Splitthoff, N, Köthe, U and Hamprecht, F A (2011). On oblique random forests. European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2011. Proceedings. Springer. 453-469 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (665.33 KB)
Pfannmöller, M, Flügge, H, Benner, G, Wacker, I, Sommer, C, Hanselmann, M, Schmale, S, Schmidt, H, Hamprecht, F A, Rabe, T, Kowalsky, W and Schröder, R (2011). Visualizing a homogeneous blend in bulk heterojunction polymer solar cells by analytical electron microscopy. Nano Letters. 11 3099-3107 DOI Google Scholar BibTeX RTF EndNote XML
Röder, J, Tolosana-Delgado, R and Hamprecht, F A (2011). Gaussian process classification: singly versus doubly stochastic models, and new computational schemes. Stochastic Environmental Research & Risk Assessment. 25 (7) 865-879 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (672.68 KB)
Schleicher, J (2011). Image Processing For Super-Resolution Localization Microscopy Utilizing An Fpga Accelerator. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Sommer, C, Straehle, C N, Köthe, U and Hamprecht, F A (2011). ilastik: Interactive Learning and Segmentation Toolkit. Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011).Proceedings. 230-233 DOI Google Scholar BibTeX RTF EndNote XML
Straehle, C N (2011). Interactive Segmentation Of Neural Electron Microscopy Data. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Straehle, C N, Köthe, U, Knott, G W and Hamprecht, F A (2011). Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images. MICCAI 2011, Proceedings. Springer. 6891 653-660 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (1.69 MB)
Wanner, S, Sommer, C, Rocholz, R, Hamprecht, F A and Jähne, B (2011). A Framework for Interactive Visualization and Classification of Dynamical Processes at the Water Surface. 16th International Workshop on Vision, Modelling and Visualization. Eurographics Association, Germany. 199-206 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (4.67 MB)

2010
Andres, B, Köthe, U, Kröger, T and Hamprecht, F A (2010). How to Extract the Geometry and Topology from Very Large 3D Segmentations. ArXiv e-prints. http://arxiv.org/abs/1009.6215 Google Scholar BibTeX RTF EndNote XML Technical Report (1.44 MB)
Andres, B, Köthe, U, Kröger, T and Hamprecht, F A (2010). Runtime-Flexible Multi-dimensional Views and Arrays for C++98 and C++0x. ArXiv e-prints. http://arxiv.org/abs/1008.2909v1 Google Scholar BibTeX RTF EndNote XML Technical Report (415.54 KB)
Andres, B, Kappes, J H, Köthe, U and Hamprecht, F A (2010). The Lazy Flipper: MAP Inference in Higher-Order Graphical Models by Depth-limited Exhaustive Search. ArXiv e-prints. http://arxiv.org/abs/1009.4102 Google Scholar BibTeX RTF EndNote XML Technical Report (625.06 KB)
Börner, K, Hermle, J, Sommer, C, Brown, N P, Knapp, B, Glass, B, Torralba, G, Reymann, J, Beil, N, Beneke, J, Pepperkok, R, Schneider, R and Ludwig, T (2010). From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication. Biotechnology Journal. 5 39-49 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (556.09 KB)
Hüsken, (2010). Active And Online Learning For Interactive Image Analysis. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Hanselmann, M (2010). Computational Methods for the Analysis of Mass Spectrometry Images. University of Heidelberg Google Scholar BibTeX RTF EndNote XML
Köthe, U, Andres, B, Kröger, T and Hamprecht, F A (2010). Geometric Analysis of 3D Electron Microscopy Data. Proceedings of Workshop on Discrete Geometry and Mathematical Morphology (WADGMM). 22-26 Google Scholar BibTeX RTF EndNote XML Technical Report (1.43 MB)
Kaster, F O, Kassemeyer, S, Merkel, B, Nix, O and Hamprecht, F A (2010). An object-oriented library for systematic training and comparison of classifiers for computer-assisted tumor diagnosis from MRSI measurements. Bildverarbeitung für die Medizin 2010 -- Algorithmen, Systeme, Anwendungen. Springer. 97-101 Google Scholar BibTeX RTF EndNote XML Technical Report (1.12 MB)

All Publications

2012

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2010

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