Publications

2014

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)
Yarkony, J, Zhang, C and Fowlkes, C C (2014). Hierarchical Planar Correlation Clustering for Cell Segmentation. EMMCVPR. Proceedings. Springer. 8932 492-504PDF icon Technical Report (548.12 KB)
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)
Blumenthal, F (2014). Information-Geometric Optimization For Image Segmentation. University of Heidelberg
Kandemir, M and Hamprecht, F A (2014). Instance Label Prediction by Dirichlet Process Multiple Instance Learning. UAI. ProceedingsPDF icon Technical Report (4.26 MB)
Straehle, C N (2014). Interactive Segmentation, Uncertainty and Learning. University of Heidelberg
Kröger, (2014). Learning-based Segmentation for Connectomics. University of Heidelberg
Kappes, J H, Beier, T and Schnörr, C (2014). MAP-Inference on Large Scale Higher-Order Discrete Graphical Models by Fusion Moves. Computer Vision - {ECCV} 2014 Workshops - Zurich, Switzerland, September 6-7 and 12, 2014, Proceedings, Part {II}. http://dx.doi.org/10.1007/978-3-319-16181-5_37PDF icon Technical Report (557.49 KB)
Urban, G, Bendszus, M, Hamprecht, F A and Kleesiek, J (2014). Multi-modal Brain Tumor Segmentation using Deep Convolutional NeuralNetworks. MICCAI BraTS (Brain Tumor Segmentation) Challenge. Proceedings, winningcontribution. 31-35
Kandemir, M, Klami, A, Gonen, M, Vetek, A and Kaski, S (2014). Multi-task and multi-view learning of user state. Neurocomputing. 139 97-106
Wieler, M (2014). Multiple Instance Learning with Random Forests and Applications in Industrial Optical Inspection. University of Heidelberg
Straehle, C N, Kandemir, M, Köthe, U and Hamprecht, F A (2014). Multiple instance learning with response-optimized random forests. ICPR. Proceedings. 3768 - 3773PDF icon Technical Report (296.66 KB)
Urban, G (2014). Neural Networks: Optimization And Applications. University of Heidelberg
Yarkony, J, Beier, T, Baldi, P and Hamprecht, F A (2014). Parallel Multicut Segmentation via Dual Decomposition. New Frontiers in Mining Complex Patterns - Third International Workshop, {NFMCP} 2014, Held in Conjunction with {ECML-PKDD} 2014, Nancy, France, September 19, 2014, Revised Selected Papers. http://dx.doi.org/10.1007/978-3-319-17876-9_4
Drory, A, Haubold, C, Avidan, S and Hamprecht, F A (2014). Semi-Global Matching: A Principled Derivation in Terms of Message Passing. GCPR. Proceedings. 43-53PDF icon Technical Report (2.6 MB)
Maco, B, Cantoni, M, Holtmaat, A, Kreshuk, A, Hamprecht, F A and Knott, G W (2014). Semiautomated Correlative 3D Electron Microscopy of In Vivo Imaged Axons and Dendrites. Nature Protocols. 9 1354-1366PDF icon Technical Report (2.01 MB)
Köthe, U, Herrmannsdörfer, F, Kats, I and Hamprecht, F A (2014). SimpleSTORM: a fast, self-calibrating reconstruction algorithm for localization microscopy. Histochemistry and Cell Biology. 141 613-627PDF icon Technical Report (2.29 MB)
Diego, F and Hamprecht, F A (2014). Sparse Space-Time Deconvolution for Calcium Image Analysis. NIPS. Proceedings. 64-72. http://papers.nips.cc/paper/5342-sparse-space-time-deconvolution-for-calcium-image-analysisPDF icon Technical Report (5.27 MB)
Lou, X, Kloft, M, Rätsch, G and Hamprecht, F A (2014). Structured Learning from Cheap Data. Advanced Structured Prediction. The MIT PressPDF icon Technical Report (8.35 MB)
Fiaschi, L, Diego, F, Grosser, K - H, Schiegg, M, Köthe, U, Zlatic, M and Hamprecht, F A (2014). Tracking indistinguishable translucent objects over time using weakly supervised structured learning. CVPR. Proceedings. 2736 - 2743PDF icon Technical Report (1.47 MB)
Zhang, C, Huber, F, Knop, M and Hamprecht, F A (2014). Yeast Cell Detection and Segmentation in Bright Field Microscopy. ISBI. Proceedings. IEEE Computer Society. 1267-1270PDF icon Technical Report (4.13 MB)

2013

Kappes, J H, Andres, B, Hamprecht, F A, Schnörr, C, Nowozin, S, Batra, D, Sungwoong, K, Kausler, B X, Lellmann, J, Komodakis, N and Rother, C (2013). A Comparative Study of Modern Inference Techniques for Discrete Energy Minimization Problems. CVPR 2013. ProceedingsPDF icon Technical Report (1.35 MB)
Röder, (2013). Active Learning: New Approaches, and Industrial Applications. University of Heidelberg
Hanslovsky, P (2013). Advanced Cell Tacking-By-Assignment. University of Heidelberg
Diego, F, Reichinnek, S, Both, M and Hamprecht, F A (2013). Automated Identification of Neuronal Activity from Calcium Imaging by Sparse Dictionary Learning. ISBI 2013. Proceedings. 1058-1061PDF icon Technical Report (2.82 MB)
Mikut, R, Dickmeis, T, Driever, W, Geurts, P, Hamprecht, F A, Kausler, B X, Ledesma-Carbayo, M, Marée, R, Mikula, K, Pantazis, P, Ronneberger, O, Santos, A and Stotzka, R (2013). Automated Processing of Zebrafish Imaging Data: A Survey. Zebrafish. 10 (3)PDF icon Technical Report (1.73 MB)
Schiegg, M, Hanslovsky, P, Kausler, B X, Hufnagel, L and Hamprecht, F A (2013). Conservation Tracking. ICCV 2013. Proceedings. 2928--2935PDF icon Technical Report (5.22 MB)
Maco, B, Holtmaat, A, Cantoni, M, Kreshuk, A, Straehle, C N, Hamprecht, F A and Knott, G W (2013). Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons. PloS one. 8 (2)PDF icon Technical Report (2.13 MB)
Wanner, S, Straehle, C N and Goldlücke, B (2013). Globally Consistent Multi-Label Assignment on the Ray Space of 4D Light Fields. CVPR 2013. Proceedings. 1011-1018
Straehle, C N, Peter, S, Köthe, U and Hamprecht, F A (2013). K-smallest Spanning Tree Segmentations. German Conference on Pattern Recognition (DAGM/GCPR). Proceedings. Springer. 375-384PDF icon Technical Report (1.18 MB)
Fiaschi, L, Grosser, K - H, Afonso, B, Zlatic, M and Hamprecht, F A (2013). Keeping Count: Leveraging Temporal Context to Count Heavily Overlapping Objects. ISBI 2013.Proceedings. 656-659PDF icon Technical Report (711.68 KB)
Walecki, R (2013). Large-Scale Automatic Reconstruction Of Myelianated Axons And Detection Of The Nodes Of Ranvier. University of Heidelberg
Fiaschi, L (2013). Learning Based Biological Image Analysis. University of Heidelberg
Diego, F and Hamprecht, F A (2013). Learning Multi-Level Sparse Representation. NIPS. Proceedings. http://papers.nips.cc/paper/5076-learning-multi-level-sparse-representationsPDF icon Technical Report (2.79 MB)
Diego, F and Hamprecht, F A (2013). Learning Multi-Level Sparse Representation for Identifying Neuronal Activity. Signal Processing with Adaptive Sparse Structured Representations Workshop (SPARS). Book of AbstractsPDF icon Technical Report (1.05 MB)
Kröger, T, Mikula, S, Denk, W, Köthe, U and Hamprecht, F A (2013). Learning to Segment Neurons with Non-local Quality Measures. MICCAI 2013. Proceedings, part II. Springer. 8150 419-427PDF icon Technical Report (2.87 MB)
Herrmannsdörfer, (2013). Simplestorm An Efficient Selfcalibrating Reconstruction Algorithm For Single And Multi-Channel Localisation Microscopy. University of Heidelberg
Kausler, B X (2013). Tracking-by-Assignment as a Probabilistic Graphical Model with Applications in Developmental Biology. University of Heidelberg
Straehle, C N, Köthe, U and Hamprecht, F A (2013). Weakly supervised learning of image partitioning using decision trees with structured split criteria. ICCV 2013. Proceedings. 1849-1856PDF icon Technical Report (5.97 MB)
Xu, B (2013). Weakly Supervised Learning: Active Schemes And Partial Annotations. University of Heidelberg

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