Publications
3
Andres, B, Köthe, U, Kröger, T, Helmstaedter, M, Briggmann, K L, Denk, W and Hamprecht, F A (2012).
3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries.
Medical Image Analysis.
16 (2012) 796-805
Technical Report (20.85 MB) A
Hanselmann, M, Röder, J, Köthe, U, Renard, B Y, Heeren, R M A and Hamprecht, F A (2012).
Active Learning for Convenient Annotation and Classification of Secondary Ion Mass Spectrometry Images.
Analytical Chemistry.
85 (1) 147-155
Technical Report (2.58 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_16 Technical Report (3.46 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) Technical Report (290.48 KB) 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
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
C
Kirchner, M, Renard, B Y, Köthe, U, Pappin, D J, Hamprecht, F A, Steen, J A J and Steen, H (2010).
Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments.
Bioinformatics.
26 (1) 77-83
Technical Report (380.19 KB) 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) D
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) Lou, X, Kirchner, M, Renard, B Y, Köthe, U, Graf, C, Lee, C, Steen, J A J, Steen, H, Mayer, M P and Hamprecht, F A (2010).
Deuteration Distribution Estimation with Improved Sequence Coverage for HX/MS Experiments.
Bioinformatics.
26(12) 1535-1541
Technical Report (518.01 KB) 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) E
Andres, B, Kondermann, C, Kondermann, D, Köthe, U, Hamprecht, F A and Garbe, C S (2008).
On errors-in-variables regression with arbitrary covariance and its application to optical flow estimation.
Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on. 1-6
Technical Report (1.58 MB) G
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) 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=mTXWsiFrci7R8tc Technical Report (534.29 KB) I
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
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
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) L
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) Pages