Browse by Research Team

Article

Validity constraints for data analysis workflows.
Schintke, F., Belhajjame, K., De Mecquenem, N., Frantz, D., Guarino, V.E., Hilbrich, M., Lehmann, F., Missier, P., Sattler, R., Sparka, J.A., Speckhard, D.T., Stolte, H., Vu, A.D. and Leser, U.
Future Generation Computer Systems 157 : 82-97. August 2024

CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting.
Graham, S., Vu, Q.D., Jahanifar, M., Weigert, M., Schmidt, U., Zhang, W., Zhang, J., Yang, S., Xiang, J., Wang, X., Rumberger, J.L., Baumann, E., Hirsch, P., Liu, L., Hong, C., Aviles-Rivero, A.I., Jain, A., Ahn, H., Hong, Y., Azzuni, H., Xu, M., Yaqub, M., Blache, M.C., Piégu, B., Vernay, B., Scherr, T., Böhland, M., Löffler, K., Li, J., Ying, W., Wang, C., Snead, D., Raza, S.E.A., Minhas, F. and Rajpoot, N.M.
Medical Image Analysis 92 : 103047. February 2024

Heat in Germany: Health risks and preventive measures.
Winklmayr, C., Matthies-Wiesler, F., Muthers, S., Buchien, S., Kuch, B., An der Heiden, M. and Mücke, H.G.
Journal of Health Monitoring 8 (S4): 3-32. 6 September 2023

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering.
Liu, C.C., Greenwald, N.F., Kong, A., McCaffrey, E.F., Leow, K.X., Mrdjen, D., Cannon, B.J., Rumberger, J.L., Varra, S.R. and Angelo, M.
Nature Communications 14 (1): 4618. 1 August 2023

A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
Meissner, G.W., Nern, A., Dorman, Z., DePasquale, G.M., Forster, K., Gibney, T., Hausenfluck, J.H., He, Y., Iyer, N.A., Jeter, J., Johnson, L., Johnston, R.M., Lee, K., Melton, B., Yarbrough, B., Zugates, C.T., Clements, Jody, Goina, C., Otsuna, H., Rokicki, K., Svirskas, R.R., Aso, Y., Card, G.M., Dickson, B.J., Ehrhardt, E., Goldammer, J., Ito, M., Kainmueller, D., Korff, W., Mais, L., Minegishi, R., Namiki, S., Rubin, G.M., Sterne, G.R., Wolff, T. and Malkesman, O.
eLife 12 : e80660. 23 February 2023

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C., Hirsch, P., Guignard, L., McDole, K., Wan, Y., Lemon, W.C., Kainmueller, D., Keller, P.J., Preibisch, S. and Funke, J.
Nature Biotechnology 44 (1): 44-49. January 2023

Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
Hönzke, K., Obermayer, B., Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E., Baumgardt, M., Löwa, A., Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M., Hinze, C., Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M., Busch, J., Klauschen, F., Horst, D., Radbruch, H., Radke, J., Heppner, F., Corman, V.M., Niemeyer, D., Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D., Landthaler, M., Ludwig, S., Suttorp, N., Witzenrath, M., Gruber, A.D., Drosten, C., Sander, L.E., Wolff, T., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 60 (6): 2102725. 1 December 2022

Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
Hirsch, P., Malin-Mayor, C., Santella, A., Preibisch, S., Kainmueller, D. and Funke, J.
Lecture Notes in Computer Science 13434 : 25-35. 16 September 2022

A comparative study of graph matching algorithms in computer vision.
Haller, S., Feineis, L., Hutschenreiter, L., Bernard, F., Rother, C., Kainmüller, D., Swoboda, P. 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., Kainmueller, D. and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

The Collaborative Research Center FONDA.
Leser, U., Hilbrich, M., Draxl, C., Eisert, P., Grunske, L., Hostert, P., Kainmüller, D., Kao, O., Kehr, B., Kehrer, T., Koch, C., Markl, V., Meyerhenke, H., Rabl, T., Reinefeld, A., Reinert, K., Ritter, K., Scheuermann, B., Schintke, F., Schweikardt, N. and Weidlich, M.
Datenbank-Spektrum 21 : 255-260. November 2021

Probabilistic deep learning for instance segmentation.
Rumberger, J.L., Mais, L. and Kainmueller, D.
Lecture Notes in Computer Science 12535 : 445-457. 2021

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites.
Veenvliet, J.V., Bolondi, A., Kretzmer, H., Haut, L., Scholze-Wittler, M., Schifferl, D., Koch, F., Guignard, L., Kumar, A.S., Pustet, M., Heimann, S., Buschow, R., Wittler, L., Timmermann, B., Meissner, A. and Herrmann, B.G.
Science 370 (6522): eaba4937. 11 December 2020

PatchPerPix for instance segmentation.
Mais, L., Hirsch, P. and Kainmueller, D.
Lecture Notes in Computer Science 12370 : 288-304. 20 November 2020

A connectome and analysis of the adult Drosophila central brain.
Scheffer, L.K., Xu, C.S., Januszewski, M., Lu, Z., Takemura, S.Y., Hayworth, K.J., Huang, G.B., Shinomiya, K., Maitlin-Shepard, J., Berg, S., Clements, J., Hubbard, P.M., Katz, W.T., Umayam, L., Zhao, T., Ackerman, D., Blakely, T., Bogovic, J., Dolafi, T., Kainmueller, D., Kawase, T., Khairy, K.A., Leavitt, L., Li, P.H., Lindsey, L., Neubarth, N., Olbris, D.J., Otsuna, H., Trautman, E.T., Ito, M., Bates, A.S., Goldammer, J., Wolff, T., Svirskas, R., Schlegel, P., Neace, E.R., Knecht, C.J., Alvarado, C.X., Bailey, D.A., Ballinger, S., Borycz, J.A., Canino, B.S., Cheatham, N., Cook, M., Dreher, M., Duclos, O., Eubanks, B., Fairbanks, K., Finley, S., Forknall, N., Francis, A., Hopkins, G.P., Joyce, E.M., Kim, S.J., Kirk, N.A., Kovalyak, J., Lauchie, S.A., Lohff, A., Maldonado, C., Manley, E.A., McLin, S., Mooney, C., Ndama, M., Ogundeyi, O., Okeoma, N., Ordish, C., Padilla, N., Patrick, C., Paterson, T., Phillips, E.E., Phillips, E.M., Rampally, N., Ribeiro, C., Robertson, M.K., Rymer, J.T., Ryan, S.M., Sammons, M., Scott, A.K., Scott, A.L., Shinomiya, A., Smith, C., Smith, K., Smith, N.L., Sobeski, M.A., Suleiman, A., Swift, J., Takemura, S., Talebi, I., Tarnogorska, D., Tenshaw, E., Tokhi, T., Walsh, J.J., Yang, T., Horne, J.A., Li, F., Parekh, R., Rivlin, P.K., Jayaraman, V., Costa, M., Jefferis, G.S.X.E., Ito, K., Saalfeld, S., George, R., Meinertzhagen, I.A., Rubin, G.M., Hess, H.F., Jain, V. and Plaza, S.M.
eLife 9 : e57443. 7 September 2020

Artificial-intelligence-driven scanning probe microscopy.
Krull, A., Hirsch, P., Rother, C., Schiffrin, A. and Krull, C.
Communications Physics 3 (1): 54. 19 March 2020

The cell adhesion protein CAR is a negative regulator of synaptic transmission.
Wrackmeyer, U., Kaldrack, J., Jüttner, R., Pannasch, U., Gimber, N., Freiberg, F., Purfürst, B., Kainmueller, D., Schmitz, D., Haucke, V., Rathjen, F.G. and Gotthardt, M.
Scientific Reports 9 (1): 6768. 1 May 2019

A benchmark for epithelial cell tracking.
Funke, J., Mais, L., Champion, A., Dye, N. and Kainmueller, D.
Lecture Notes in Computer Science 11134 : 437-445. 23 January 2019

Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
Dye, N.A., Popović, M., Spannl, S., Etournay, R., Kainmüller, D., Ghosh, S., Myers, E.W., Jülicher, F. and Eaton, S.
Development 144 (23): 4406-4421. 1 December 2017

GPU-accelerated level-set segmentation.
Lamas-Rodríguez, J., Heras, D.B., Argüello, F., Kainmueller, D., Zachow, S. and Bóo, M.
Journal of Real-Time Image Processing 12 (1): 15-29. June 2016

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
Stapel, L.C., Lombardot, B., Broaddus, C., Kainmueller, D., Jug, F., Myers, E.W. and Vastenhouw, N.L.
Development 143 (3): 540-546. 1 February 2016

Uncertainty-driven forest predictors for vertebra localization and segmentation.
Richmond, D., Kainmueller, D., Glocker, B., Rother, C. and Myers, G.
Lecture Notes in Computer Science 9349 : 653-660. 2015

Active graph matching for automatic joint segmentation and annotation of C. elegans.
Kainmueller, D., Jug, F., Rother, C. and Myers, G.
Lecture Notes in Computer Science 8673 : 81-88. 2014

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

Omnidirectional displacements for deformable surfaces.
Kainmueller, D., Lamecker, H., Heller, M.O., Weber, B., Hege, H.C. and Zachow, S.
Medical Image Analysis 17 (4): 429-441. May 2013

Automatic detection and classification of teeth in CT data.
Duy, N.T., Lamecker, H., Kainmueller, D. and Zachow, S.
Lecture Notes in Computer Science 7510 : 609-616. 2012

An articulated statistical shape model of the human knee.
Bindernagel, M., Kainmueller, D., Seim, H., Lamecker, H., Zachow, S. and Hege, H.C.
Informatik aktuell : 59-63. 2011

3D reconstruction of the human rib cage from 2D projection images using a statistical shape model.
Dworzak, J., Lamecker, H., von Berg, J., Klinder, T., Lorenz, C., Kainmüller, D., Seim, H., Hege, H.C. and Zachow, S.
International Journal of Computer Assisted Radiology and Surgery 5 (2): 111-124. March 2010

Improving deformable surface meshes through omni-directional displacements and MRFs.
Kainmueller, D., Lamecker, H., Seim, H., Zachow, S. and Hege, H.C.
Lecture Notes in Computer Science 6361 : 227-234. 2010

Comparison and evaluation of methods for liver segmentation from CT datasets.
Heimann, T., van Ginneken, B., Styner, M.A., Arzhaeva, Y., Aurich, V., Bauer, C., Beck, A., Becker, C., Beichel, R., Bekes, G., Bello, F., Binnig, G., Bischof, H., Bornik, A., Cashman, P.M.M., Chi, Y., Cordova, A., Dawant, B.M., Fidrich, M., Furst, J.D., Furukawa, D., Grenacher, L., Hornegger, J., Kainmüller, D., Kitney, R.I., Kobatake, H., Lamecker, H., Lange, T., Lee, J., Lennon, B., Li, R., Li, S., Meinzer, H.P., Nemeth, G., Raicu, D.S., Rau, A.M., van Rikxoort, E.M., Rousson, M., Rusko, L., Saddi, K.A., Schmidt, G., Seghers, D., Shimizu, A., Slagmolen, P., Sorantin, E., Soza, G., Susomboon, R., Waite, J.M., Wimmer, A. and Wolf, I.
IEEE Transactions on Medical Imaging 28 (8): 1251-1265. August 2009

Automatic extraction of mandibular nerve and bone from cone-beam CT data.
Kainmueller, D., Lamecker, H., Seim, H., Zinser, M. and Zachow, S.
Lecture Notes in Computer Science 5762 : 76-83. 2009

Coupling deformable models for multi-object segmentation.
Kainmueller, D., Lamecker, H., Zachow, S. and Hege, H.C.
Lecture Notes in Computer Science 5104 : 69-78. 2008

Level set segmentation of the heart from 4D phase contrast MRI.
Kainmuller, D., Unterhinninghofen, R., Ley, S. and Dillmann, R.
Proceedings of SPIE 6914 : 691414. 2008

Book Section

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P., Epstein, L. and Guignard, L.
In: Cell Movement in Health and Disease. Academic Press, London, 341-361. ISBN 978-0-323-90195-6 2022

Conference or Workshop Item

Simultaneous lung cell and nucleus segmentation from labelled versus unlabelled human lung DIC images.
Dohmen, M., Mittermaier, M., Rumberger, J.L., Yang, L.L., Gruber, A.D., Toennies, M., Hippenstiel, S., Kainmueller, D. and Hocke, A.C.
In: 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 27-30 May 2024, Athens, Greece. 22 August 2024

Model guidance via explanations turns image classifiers into segmentation models.
Yu, X., Franzen, J., Samek, W., Höhne, M.M.C. and Kainmueller, D.
In: Second World Conference, xAI 2024, July 17–19, 2024, Valletta, Malta. 10 July 2024

TLIMB - a transfer learning framework for image analysis of the brain.
Schulz, M.A., Albrecht, J.P., Yilmaz, A., Koch, A., Kainmüller, D., Leser, U. and Ritter, K.
In: Workshops of the EDBT/ICDT 2024 Joint Conference, EDBT/ICDT-WS 2024, 25-28 March 2024, Paestum, Italy. 25 March 2024

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L., Franzen, J., Hirsch, P., Albrecht, J.P. and Kainmueller, D.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Towards hierarchical regional transformer-based multiple instance learning.
Cersovsky, J., Mohammadi, S., Kainmueller, D. and Hoehne, J.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L., Baumann, E., Hirsch, P., Janowczyk, A., Zlobec, I. and Kainmueller, D.
In: 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 28-31 March 2022, Kolkata, India. 17 August 2022

Fusion moves for graph matching.
Hutschenreiter, L., Haller, S., Feineis, L., Rother, C., Kainmüller, D. and Savchynskyy, B.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

How shift equivariance impacts metric learning for instance segmentation.
Rumberger, J.L., Yu, X., Hirsch, P., Dohmen, M., Guarino, V.E., Mokarian, A., Mais, L., Funke, J. and Kainmueller, D.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

A convex relaxation for multi-graph matching.
Swoboda, P., Kainmüller, D., Mokarian, A., Theobalt, C. and Bernard, F.
In: 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 16-20 Jun 2019, Long Beach, CA, USA. 2019

A study of Lagrangean decompositions and dual ascent solvers for graph matching.
Swoboda, P., Rother, C., Alhaija, H.A., Kainmüller, D. and Savchynskyy, B.
In: 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 21-26 Jul 2017, Honolulu, HI, USA. 9 November 2017

Crowd sourcing image segmentation with iaSTAPLE.
Schlesinger, D., Jug, F., Myers, G., Rother, C. and Kainmueller, D.
In: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 18-21 Apr 2017, Melbourne, VIC, Australia. 19 June 2017

Mapping auto-context decision forests to deep ConvNets for semantic segmentation.
Richmond, D., Kainmueller, D., Yang, M., Myers, E. and Rother, C.
In: 27th British Machine Vision Conference, BMVC 2016, 19-22 Sep 2016, York, United Kingdom. September 2016

Convexity shape constraints for image segmentation.
Royer, L.A., Richmond, D.L., Rother, C., Andres, B. and Kainmueller, D.
In: IEEE Conference on Computer Vision and Pattern Recognition, 27-30 Jun 2016, Las Vegas, USA. 2016

Partitioning and mapping a fast level-set algorithm on the GPU.
Lamas-Rodriguez, J., Heras, D.B., Arguello, F., Zachow, S. and Kainmueller, D.
In: The 7th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications, 12-14 Sept 2013, Berlin, Germany. 2013

An articulated statistical shape model for accurate hip joint segmentation.
Kainmueller, D., Lamecker, H., Zachow, S. and Hege, H.C.
In: 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 3-6 Sep 2009, Minneapolis, MN, USA. 13 September 2009

A system for unsupervised extraction of orthopedic parameters from CT data.
Seim, H., Kainmüller, D., Lamecker, H. and Zachow, S.
In: INFORMATIK 2009 Im Fokus das Leben: 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28 Sept - 2 Oct 2009, Lübeck, Germany. 2009

Automatic extraction of anatomical landmarks from medical image data: An evaluation of different methods.
Seim, H., Kainmueller, D., Heller, M., Zachow, S. and Hege, H.C.
In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 28 Jun - 1 Jul 2009, Bosten, USA. 2009

Automatic segmentation of the pelvic bones from CT data based on a statistical shape model.
Seim, H., Kainmueller, D., Heller, M., Lamecker, H., Zachow, S. and Hege, H.C.
In: VCBM 08: Eurographics Workshop on Visual Computing for Biomedicine, 6-7 Oct 2008, Delft, Netherlands. 2008

Book

Deformable meshes for medical image segmentation.
Kainmueller, D.
Aktuelle Forschung Medizintechnik - Latest Research in Medical Engineering . Springer Vieweg, Wiesbaden. ISBN 978-3-658-07014-4 2015

Review

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A., Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M., Heckmann-Nötzel, D., Rädsch, T., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Blaschko, M.B., Cardoso, M.J., Cheplygina, V., Cimini, B.A., Collins, G.S., Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Haase, R., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Karthikesalingam, A., Kofler, F., Kopp-Schneider, A., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G., Madani, A., Maier-Hein, K., Martel, A.L., Mattson, P., Meijering, E., Menze, B., Moons, K.G.M., Müller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rajpoot, N., Rieke, N., Saez-Rodriguez, J., Sánchez, C.I., Shetty, S., van Smeden, M., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Van Calster, B., Varoquaux, G. and Jäger, P.F.
Nature Methods 21 (2): 195-212. 12 February 2024

Understanding metric-related pitfalls in image analysis validation.
Reinke, A., Tizabi, M.D., Baumgartner, M., Eisenmann, M., Heckmann-Nötzel, D., Kavur, A.E., Rädsch, T., Sudre, C.H., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Buettner, F., Cardoso, M.J., Cheplygina, V., Chen, J., Christodoulou, E., Cimini, B.A., Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Glocker, B., Godau, P., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Isensee, F., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Kleesiek, J., Kofler, F., Kooi, T., Kopp-Schneider, A., Kozubek, M., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G., Madani, A., Maier-Hein, K., Martel, A.L., Meijering, E., Menze, B., Moons, K.G.M., Müller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rafelski, S.M., Rajpoot, N., Reyes, M., Riegler, M.A., Rieke, N., Saez-Rodriguez, J., Sánchez, C.I., Shetty, S., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Van Calster, B., Varoquaux, G., Yaniv, Z.R., Jäger, P.F. and Maier-Hein, L.
Nature Methods 21 (2): 182–194. February 2024

Letter

Plasma mediators in patients with severe COVID-19 cause lung endothelial barrier failure.
Michalick, L., Weidenfeld, S., Grimmer, B., Fatykhova, D., Solymosi, P.D., Behrens, F., Dohmen, M., Brack, M.C., Schulz, S., Thomasch, E., Simmons, S., Müller-Redetzky, H., Suttorp, N., Kurth, F., Neudecker, J., Toennies, M., Bauer, T.T., Eggeling, S., Corman, V.M., Hocke, A.C., Witzenrath, M., Hippenstiel, S. and Kuebler, W.M.
European Respiratory Journal 57 (3): 2002384. 11 March 2021

Preprint

Do transformers and CNNs learn different concepts of brain age?
Siegel, N.T., Kainmueller, D., Deniz, F., Ritter, K. and Schulz, M.A.
bioRxiv : 2024.08.09.607321. 9 August 2024

PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L., Hirsch, P., Managan, C., Wang, K., Rokicki, K., Svirskas, R.R., Dickson, B.J., Korff, W., Rubin, G.M., Ihrke, G., Meissner, G.W. and Kainmueller, D.
bioRxiv : 2021.07.23.453511. 26 July 2021