Publications
Book Chapter
Haubold, C, Schiegg, M, Kreshuk, A, Berg, S, Köthe, U and Hamprecht, F A (2016).
Segmenting and Tracking Multiple Dividing Targets Using ilastik.
Focus on Bio-Image Informatics. Springer.
219 199-229
Technical Report (4.46 MB) Conference Paper
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_16 Technical Report (3.46 MB) Kreshuk, A, Straehle, C N, Sommer, C, Köthe, U, Knott, G W and Hamprecht, F A (2011).
Automated Segmentation of Synapses in 3D EM Data.
Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011).
Proceedings. 220-223
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.2014.17 Technical Report (10.06 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
Technical Report (1.44 MB) 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
Technical Report (809.07 KB) 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
Technical Report (1.43 MB) 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
Technical Report (1.43 MB) Andres, B, Kröger, T, Briggmann, K L, Denk, W, Norogod, N, Knott, G W, Köthe, U and Hamprecht, F A (2012).
Globally Optimal Closed-Surface Segmentation for Connectomics.
ECCV 2012. Proceedings, Part 3. 778-791
Technical Report (2.72 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. 12-17
Technical Report (405.91 KB) 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
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. 536-539
Technical Report (2.25 MB) 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. 375-384
Technical Report (1.18 MB) Andres, B, Kappes, J H, Beier, T, Köthe, U and Hamprecht, F A (2012).
The Lazy Flipper: Efficient Depth-Limited Exhaustive Search in Discrete Graphical Models.
Computer Vision - {ECCV} 2012 - 12th European Conference on Computer Vision, Florence, Italy, October 7-13, 2012, Proceedings, Part {VII}.
http://dx.doi.org/10.1007/978-3-642-33786-4_12 Technical Report (446.28 KB) Hanselmann, M, Köthe, U, Renard, B Y, Kirchner, M, Heeren, R M A and Hamprecht, F A (2009).
Multivariate Watershed Segmentation of Compositional Data.
Proceedings of the 15th International Conference on Discrete Geometry for Computer Imagery (DGCI), in press. Springer.
5810 180-192
Technical Report (1.25 MB) 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.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
11208 LNCS 571–587.
http://arxiv.org/abs/1904.12654 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
Technical Report (665.33 KB) Adler, T J, Ayala, L, Ardizzone, L, Kenngott, H G, Vemuri, A, Müller-Stich, B P, Rother, C, Köthe, U and Maier-Hein, L (2019).
Out of Distribution Detection for Intra-operative Functional Imaging.
MICCAI UNSURE Workshop 2019.
11840 LNCS 75–82
PDF (3.1 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. 394-398
Technical Report (648.55 KB) Andres, B, Köthe, U, Bonea, A, Nadler, B and Hamprecht, F A (2009).
Quantitative Assessment of Image Segmentation Quality by Random Walk Relaxation Times.
Pattern Recognition. 31st DAGM Symposium, Jena, Germany, September 9-11, 2009. Proceedings. Springer.
5748 502-511
Technical Report (3.08 MB) Andres, B, Köthe, U, Helmstaedter, M, Denk, W and Hamprecht, F A (2008).
Segmentation of SBFSEM Volume Data of Neural Tissue by Hierarchical Classification.
Pattern Recognition. 30th DAGM Symposium Munich, Germany, June 10-13, 2008. Proceedings. Springer.
5096 142-152
Technical Report (1.21 MB) Pages