2025

MAGO-SP: detection and correction of water-fat swaps in magnitude-only VIBE MRI.
Graf, Robert ORCID: https://orcid.org/0000-0001-6656-3680, Möller, Hendrik, Starck, Sophie, Atad, Matan, Braun, Philipp, Stelter, Jonathan, Peters, Annette, Krist, Lilian, Willich, Stefan N., Völzke, Henry, Bülow, Robin, Pischon, Tobias ORCID: https://orcid.org/0000-0003-1568-767X, Niendorf, Thoralf ORCID: https://orcid.org/0000-0001-7584-6527, Paetzold, Johannes C., Karampinos, Dimitrios, Rueckert, Daniel and Kirschke, Jan
Lecture Notes in Computer Science 15972 : 328-338. 20 September 2025

PathoCellBench: A comprehensive benchmark for cell phenotyping.
Lüscher, Jérôme, Koreuber, Nora ORCID: https://orcid.org/0009-0003-9328-4590, Franzen, Jannik ORCID: https://orcid.org/0000-0002-0761-641X, Reith, Fabian H. ORCID: https://orcid.org/0000-0002-0745-2726, Winklmayr, Claudia ORCID: https://orcid.org/0000-0002-8784-2301, Baumann, Elias, Schürch, Christian M., Kainmüller, Dagmar ORCID: https://orcid.org/0000-0002-9830-2415 and Rumberger, Josef Lorenz ORCID: https://orcid.org/0000-0002-7225-7011
Lecture Notes in Computer Science 15966 : 411-420. 20 September 2025

Detecting unforeseen data properties with diffusion autoencoder embeddings using spine MRI data.
Graf, R., Hunecke, F., Pohl, S., Atad, M., Moeller, H., Starck, S., Kroencke, T., Bette, S., Bamberg, F., Pischon, T. ORCID: https://orcid.org/0000-0003-1568-767X, Niendorf, T. ORCID: https://orcid.org/0000-0001-7584-6527, Schmidt, C., Paetzold, J.C., Rueckert, D. and Kirschke, J.S.
Lecture Notes in Computer Science 2024 (15274): 79-88. 17 January 2025

2024

Solving the inverse problem of microscopy deconvolution with a residual Beylkin-Coifman-Rokhlin neural network.
Li, R. ORCID: https://orcid.org/0000-0002-3085-5267, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, A.
Lecture Notes in Computer Science 15133 : 378-395. 1 November 2024

The (un)answered question: a data science powered music experiment.
von Kurnatowski, L. ORCID: https://orcid.org/0000-0001-5144-702X, Wolff, B., Kernchen, S. ORCID: https://orcid.org/0009-0005-4430-6743, Klapproth-Rieger, A. ORCID: https://orcid.org/0000-0002-9361-5025, Heidrich, D. ORCID: https://orcid.org/0000-0002-8501-5089, Haupt, C. ORCID: https://orcid.org/0000-0001-6447-1379, Schreiber, A. ORCID: https://orcid.org/0000-0001-5750-5649, Niendorf, T. ORCID: https://orcid.org/0000-0001-7584-6527, Kosmider, A., Lobbes, M. and Hennecke, M.
Lecture Notes in Computer Science 14717 : 233-246. 2 June 2024

Decoil: reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data.
Giurgiu, M. ORCID: https://orcid.org/0000-0001-5007-7442, Wittstruck, N. ORCID: https://orcid.org/0009-0000-4378-3226, Rodriguez-Fos, E. ORCID: https://orcid.org/0000-0002-2555-0178, Chamorro González, R. ORCID: https://orcid.org/0000-0002-5653-7259, Brückner, L. ORCID: https://orcid.org/0000-0002-6155-2277, Krienelke-Szymansky, A. ORCID: https://orcid.org/0000-0003-4797-4526, Helmsauer, K. ORCID: https://orcid.org/0000-0003-0773-4114, Hartebrodt, A. ORCID: https://orcid.org/0000-0002-9172-3137, Euskirchen, P. ORCID: https://orcid.org/0000-0002-9138-805X, Koche, R.P. ORCID: https://orcid.org/0000-0002-6820-5083, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Reinert, K. ORCID: https://orcid.org/0000-0003-3078-8129 and Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X
Lecture Notes in Computer Science 14758 : 406-411. 17 May 2024

2022

Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
Hirsch, P. ORCID: https://orcid.org/0000-0002-2353-5310, Malin-Mayor, C. ORCID: https://orcid.org/0000-0002-9627-6030, Santella, A., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415 and Funke, J. ORCID: https://orcid.org/0000-0003-4388-7783
Lecture Notes in Computer Science 13434 : 25-35. 16 September 2022

A comparative study of graph matching algorithms in computer vision.
Haller, S. ORCID: https://orcid.org/0000-0002-0855-8549, Feineis, L., Hutschenreiter, L., Bernard, F., Rother, C., Kainmüller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Swoboda, P. ORCID: https://orcid.org/0000-0003-4065-8758 and Savchynskyy, B.
Lecture Notes in Computer Science 13683 : 636-653. 2022

Data augmentation via partial nonlinear registration for brain-age prediction.
Schulz, M.A., Koch, A., Guarino, V.E. ORCID: https://orcid.org/0000-0003-1625-4323, Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415 and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

2021

DenoiSeg: joint denoising and segmentation.
Buchholz, T.O. ORCID: https://orcid.org/0000-0001-6953-8915, Prakash, M. ORCID: https://orcid.org/0000-0002-6351-0281, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Krull, A. ORCID: https://orcid.org/0000-0002-7778-7169 and Jug, F. ORCID: https://orcid.org/0000-0002-8499-5812
Lecture Notes in Computer Science 12535 : 324-337. 10 January 2021

Bionic tracking: using eye tracking to track biological cells in virtual reality.
Günther, U. ORCID: https://orcid.org/0000-0002-1179-8228, Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Dachselt, R. ORCID: https://orcid.org/0000-0002-2176-876X and Sbalzarini, I.F. ORCID: https://orcid.org/0000-0003-4414-4340
Lecture Notes in Computer Science 12535 : 280-297. 2021

Probabilistic deep learning for instance segmentation.
Rumberger, J.L. ORCID: https://orcid.org/0000-0002-7225-7011, Mais, L. ORCID: https://orcid.org/0000-0002-9281-2668 and Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415
Lecture Notes in Computer Science 12535 : 445-457. 2021

2020

PatchPerPix for instance segmentation.
Mais, L. ORCID: https://orcid.org/0000-0002-9281-2668, Hirsch, P. ORCID: https://orcid.org/0000-0002-2353-5310 and Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415
Lecture Notes in Computer Science 12370 : 288-304. 20 November 2020

2019

3D high resolution imaging of human heart for visualization of the cardiac structure.
Haliot, K., Magat, J., Ozenne, V., Abell, E., Dubes, V., Bear, L., Gilbert, S.H. ORCID: https://orcid.org/0000-0002-1997-1689, Trew, M.L., Haissaguerre, M., Quesson, B. and Bernus, O.
Lecture Notes in Computer Science 11504 : 196-207. 30 May 2019

A benchmark for epithelial cell tracking.
Funke, J., Mais, L. ORCID: https://orcid.org/0000-0002-9281-2668, Champion, A., Dye, N. and Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415
Lecture Notes in Computer Science 11134 : 437-445. 23 January 2019

Fast cross correlation for limited angle tomographic data.
Sánchez, R.M., Mester, R. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Lecture Notes in Computer Science 11482 : 415-426. 2019

2018

A semi-supervised approach to discover bivariate causality in large biological data.
Sokolovska, N., Permiakova, O., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Zucker, J.D.
Lecture Notes in Computer Science 10934 : 406-420. 8 July 2018

Understanding chromatin structure: efficient computational implementation of polymer physics models.
Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Annunziatella, C., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fiorillo, L., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Campanile, R. and Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167
Lecture Notes in Computer Science 11339 : 680-691. 2018

2015

Reproducible and user-controlled software environments in HPC with Guix.
Courtes, L. and Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189
Lecture Notes in Computer Science 9523 : 579-591. 2015

Uncertainty-driven forest predictors for vertebra localization and segmentation.
Richmond, D., Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Glocker, B., Rother, C. and Myers, G.
Lecture Notes in Computer Science 9349 : 653-660. 2015

2014

Optimal joint segmentation and tracking of escherichia coli in the mother machine.
Jug, F., Pietzsch, T., Kainmüller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Funke, J., Kaiser, M., van Nimwegen, E., Rother, C. and Myers, G.
Lecture Notes in Computer Science 8677 : 25-36. 2014

Active graph matching for automatic joint segmentation and annotation of C. elegans.
Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Jug, F., Rother, C. and Myers, G.
Lecture Notes in Computer Science 8673 : 81-88. 2014

Bridging the Gap: Methods and Teaching of F-A-S-T - Framing-Art-Science-Technology.
Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Koalick, G., Gassel, S., Sery, C., Groh, R. and Wacker, M.
Lecture Notes in Computer Science 8517 : 589-600. 2014

2012

Automatic detection and classification of teeth in CT data.
Duy, N.T., Lamecker, H., Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415 and Zachow, S.
Lecture Notes in Computer Science 7510 : 609-616. 2012

Prediction of transcription factor binding sites by integrating DNase digestion and histone modification.
Gusmao, E.G., Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311 and Costa, I.G.
Lecture Notes in Computer Science 7409 : 109-119. 2012

2010

Improving deformable surface meshes through omni-directional displacements and MRFs.
Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Lamecker, H., Seim, H., Zachow, S. and Hege, H.C.
Lecture Notes in Computer Science 6361 : 227-234. 2010

In silico screening for pathogenesis related-2 gene candidates in Vigna uguiculata transcriptome.
Wanderley-Nogueira, A.C., Da Mota Soares-Cavalcanti, N., Belarmino, L.C., Barbosa-Silva, A. ORCID: https://orcid.org/0000-0002-5260-2607, Kido, E.A., Do Monte, S.J.H., Pandolfi, V., Calsa-Junior, T. and Benko-Iseppon, A.M.
Lecture Notes in Computer Science 6160 : 70-81. 2010

2009

Automatic extraction of mandibular nerve and bone from cone-beam CT data.
Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Lamecker, H., Seim, H., Zinser, M. and Zachow, S.
Lecture Notes in Computer Science 5762 : 76-83. 2009

2008

Constructing phylogenetic supernetworks from quartets.
Grünewald, S., Spillner, A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Moulton, V.
Lecture Notes in Computer Science 5251 : 284-295. 2008

Coupling deformable models for multi-object segmentation.
Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Lamecker, H., Zachow, S. and Hege, H.C.
Lecture Notes in Computer Science 5104 : 69-78. 2008

A customized class of functions for modeling and clustering gene expression profiles in embryonic stem cells.
Li, S., Andrade-Navarro, M. ORCID: https://orcid.org/0000-0001-6650-1711 and Sankoff, D.
Lecture Notes in Computer Science 5167 : 92-103. 2008

2007

Adaptive multi-modal sensors.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Siegelmann, H.T.
In: 50 years of artificial intelligence. Lecture Notes in Computer Science, 4850 (4850). Springer, Berlin, Heidelberg, 164-173. ISBN 978-3-540-77295-8 2007

2005

Detecting functional modules of transcription factor binding sites in the human genome.
Manke, T., Dieterich, C. and Vingron, M.
Lecture Notes in Computer Science 3318 : 14-21. 2005

2004

Suboptimal local alignments across multiple scoring schemes.
Michael, M., Dieterich, C. and Stoye, J.
Lecture Notes in Computer Science 3240 : 99-110. 2004

1999

Information theoretic based segments for language identification.
Harbeck, S., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Noth, E. and Niemann, H.
Lecture Notes in Computer Science 1692 : 187-192. 1999