Publications
2012
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) 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) 2014
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) 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) 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) 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 - 2743
Technical Report (1.47 MB) 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
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) 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) 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) 2016
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) Kleesiek, J, Petersen, J, Döring, M, Maier-Hein, K, Köthe, U, Wick, W, Hamprecht, F A, Bendszus, M and Biller, A (2016).
Virtual Raters for Reproducible and Objective Assessments in Radiology.
Nature Scientific Reports.
6 Technical Report (2.81 MB) 2017
Beier, T, Pape, C, Rahaman, N, Prange, T, Berg, S, Bock, D, Cardona, A, Knott, G W, Plaza, S M, Scheffer, L K, Köthe, U, Kreshuk, A and Hamprecht, F A (2017).
Multicut brings automated neurite segmentation closer to human performance.
Nature Methods.
14 101-102.
http://rdcu.be/oVDQ Krasowki, N, Beier, T, Knott, G W, Köthe, U, Hamprecht, F A and Kreshuk, A (2017).
Neuron Segmentation with High-Level Biological Priors.
IEEE Transactions on Medical Imaging.
37 2018
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.
ECCV. Proceedings. Springer. 571-587
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 2019
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
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
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