Ronneberger's with Publications

Deep learning is widely applicable to phenotyping embryonic development and disease doi>

T. Naert, Ö. Cicek, P. Ogar, M. Buergi, N. Shaidani, M. Kaminski, Y. Xu, K. Grand, M. Vujanovic, D. Prata, F. Hildebrandt, Thomas Brox, Olaf Ronneberger, F. Voigt, F. Helmchen, J. Loffing, M. Horb, H. Willsey, S. Lienkamp

Development, 148(21), 2021

U-Net – Deep Learning for Cell Counting, Detection, and Morphometry Paper

doi> Project

Thorsten Falk, Dominic Mai, Robert Bensch, Özgün Çiçek, Ahmed Abdulkadir, Yassine Marrakchi, Anton Böhm, J. Deubner, Z. Jäckel, K. Seiwald, A. Dovzhenko, O. Tietz, C. Dal Bosco, S. Walsh, D. Saltukoglu, T. Tay, M. Prinz, K. Palme, M. Simons, I. Diester, Thomas Brox, Olaf Ronneberger

Nature Methods, 16: 67-70, 2019

Clinically applicable deep learning for diagnosis and referral in retinal disease Paper

paper-De_Fauw_et_al_2018_Nature_Medicine.pdf

doi> Code/data

J. De Fauw, J. Ledsam, B. Romera-Paredes, S. Nikolov, N. Tomasev, S. Blackwell, H. Askham, X. Glorot, B. O’Donoghue, D. Visentin, G. van den Driessche, B. Lakshminarayanan, C. Meyer, F. Mackinder, S. Bouton, K. Ayoub, R. Chopra, D. King, A. Karthikesalingam, C. Hughes, R. Raine, J. Hughes, D. Sim, C. Egan, A. Tufail, H. Montgomery, D. Hassabis, G. Rees, T. Back, P. Khaw, M. Suleyman, J. Cornebise, P. Keane, Olaf Ronneberger

Nature Medicine, 24(9): 1342--1350, 2018

Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake doi> Code/data

A. Middleton, C. Dal Bosco, P. Chlap, Robert Bensch, H. Harz, F. Ren, S. Bergmann, S. Wend, W. Weber, K. Hayashi, M. Zurbriggen, R. Uhl, Olaf Ronneberger, K. Palme, C. Fleck, A. Dovzhenko

Cell Reports, 22(11): 3044--3057, Mar 2018

A Probabilistic U-Net for Segmentation of Ambiguous Images Paper

7928-a-probabilistic-u-net-for-segmentation-of-ambiguous-images.pdf

S. Kohl, B. Romera-Paredes, C. Meyer, J. De Fauw, J. Ledsam, K. Maier-Hein, S. Eslami, D. Jimenez Rezende, Olaf Ronneberger

32nd Conference on Neural Information Processing Systems (NeurIPS), Dec 2018

ISOO_DL: Instance segmentation of overlapping biological objects using deep learning Paper

paper-ISBI18_ISOO_final_030118_IEEE_CR.pdf

doi>

Anton Böhm, A. Ücker, T. Jäger, Olaf Ronneberger, Thorsten Falk

15th International Symposium on Biomedical Imaging (ISBI), IEEE: 1225--1229, 2018

Deep learning to achieve clinically applicable segmentation of head and neck anatomy for radiotherapy Paper

S. Nikolov, S. Blackwell, R. Mendes, J. De Fauw, C. Meyer, C. Hughes, H. Askham, B. Romera-Paredes, A. Karthikesalingam, C. Chu, D. Carnell, C. , D. D'Souza, S. Moinuddin, K. Sullivan, D. Consortium, H. Montgomery, G. Rees, R. Sharma, M. Suleyman, T. Back, J. Ledsam, Olaf Ronneberger

Technical Report , arXiv:1809.04430, Sep 2018

A 3D digital atlas of the Nicotiana tabacum root tip and its use to investigate changes in the root apical meristem induced by the Agrobacterium 6b oncogene doi>

T. Pasternak, T. Haser, Thorsten Falk, Olaf Ronneberger, K. Palme, L. Otten

The Plant Journal, 92(1): 31--42, Aug 2017

A new fate mapping system reveals context-dependent random or clonal expansion of microglia doi>

T. Leng Tay, Dominic Mai, J. Dautzenberg, F. Fernández-Klett, G. Lin, S. , M. Datta, A. Drougard, T. Stempfl, A. Ardura-Fabregat, O. Staszewski, A. Margineanu, A. Sporbert, L. M Steinmetz, J. Andrew Pospisilik, S. Jung, J. Priller, D. Grün, Olaf Ronneberger, M. Prinz

Nature Neuroscience, 2017

An objective comparison of cell-tracking algorithms doi>

V. Ulman, M. Maška, K. Magnusson, Olaf Ronneberger, C. Haubold, N. Harder, P. Matula, P. Matula, D. Svoboda, M. Radojevic, I. Smal, K. Rohr, J. Jaldén, H. Blau, O. Dzyubachyk, B. Lelieveldt, P. Xiao, Y. Li, S. Cho, A. Dufour, J. Olivo-Marin, C. Reyes-Aldasoro, J. Solis-Lemus, Robert Bensch, Thomas Brox, J. Stegmaier, R. Mikut, S. Wolf, F. Hamprecht, T. Esteves, P. Quelhas, Ö. Demirel, L. Malmström, F. Jug, P. Tomancák, E. Meijering, A. Muñoz-Barrutia, M. Kozubek, C. Ortiz-de-Solor

Nature Methods, 14: 1141-1152, 2017

Gland segmentation in colon histology images: The glas challenge contest doi>

K. Sirinukunwattana, J. Pluim, H. Chen, X. Qi, P. Heng, Y. Guo, L. Wang, B. Matuszewski, E. Bruni, U. Sanchez, Anton Böhm, Olaf Ronneberger, B. Cheikh, D. Racoceanu, P. Kainz, M. Pfeiffer, M. Urschler, D. Snead, N. Rajpoot

Medical Image Analysis, 35: 489-502, 2017

Spatiotemporal Deformable Prototypes for Motion Anomaly Detection doi> Code/data

Robert Bensch, N. Scherf, J. Huisken, Thomas Brox, Olaf Ronneberger

International Journal of Computer Vision, 122(3): 502--523, May 2017

A benchmark for comparison of dental radiography analysis algorithms doi>

C. Wang, C. Huang, J. Lee, C. Li, S. Chang, M. Siao, T. Lai, B. Ibragimov, T. Vrtovec, Olaf Ronneberger, Philipp Fischer, T. Cootes, C. Lindner

Medical Image Analysis, 31: 63-76, Jul 2016

3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation Paper

doi> Code/data

Özgün Çiçek, Ahmed Abdulkadir, S. Lienkamp, Thomas Brox, Olaf Ronneberger

Medical Image Computing and Computer-Assisted Intervention (MICCAI), Springer, LNCS, Vol.9901: 424--432, Oct 2016

B cell antigen receptors of class IgM and IgD are clustered in different protein islands that are altered during B cell activation doi>

P. Maity, A. Blount, H. Jumaa, Olaf Ronneberger, B. Lillemeier, M. Reth

Science Signalling, 8(394): ra93, 2015

Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: The CADDementia challenge doi>

E. Bron, M. Smits, W. van der Flier, H. Vrenken, F. Barkhof, P. Scheltens, J. Papma, R. Steketee, C. M\'{e}ndez Orellana, R. Meijboom, M. Pinto, J. Meireles, C. Garrett, A. Bastos-Leite, Ahmed Abdulkadir, Olaf Ronneberger, N. Amoroso, R. Bellotti, D. C\'{a}rdenas-Pe\~{n}a, A. \'{A}lvarez-Meza, C. Dolph, K. Iftekharuddin, S. Eskildsen, P. Coup\'{e}, V. Fonov, K. Franke, C. Gaser, C. Ledig, R. Guerrero, T. Tong, K. Gray, E. Moradi, J. Tohka, A. Routier, S. Durrleman, A. Sarica, G. Di Fatta, F. Sensi, A. A

NeuroImage, 111: 562–-579, May 2015

Spontaneous and electric field-controlled front-rear polarization of human keratinocytes doi>

D. Saltukoglu, J. Grünewald, N. Strohmeyer, Robert Bensch, M. Ulbrich, Olaf Ronneberger, M. Simons

Molecular Biology of the Cell, 26(24): 4373--4386, Dec 2015

The polarity protein Inturned links NPHP4 to Daam1 to control the subapical actin network in multiciliated cells doi>

T. Yasunaga, S. Hoff, C. Schell, M. Helmstädter, O. Kretz, S. Kuechlin, T. Yakulov, C. Engel, B. Müller, Robert Bensch, Olaf Ronneberger, T. Huber, S. Lienkamp, G. Walz

Journal of Cell Biology, 211(5): 963--973, 2015

Modelling Two-Phase Flow in a Micro-Model with Local Thermal Non-Equilibrium on the Darcy Scale doi>

P. Nuske, Olaf Ronneberger, N. Karadimitriou, R. Helmig, S. Hassanizadeh

International Journal of Heat and Mass Transfer, 88: 822--835, 2015

The Rac1 regulator ELMO controls basal body migration and docking in multiciliated cells through interaction with Ezrin doi>

D. Epting, K. Slanchev, C. Boehlke, S. Hoff, N. Loges, T. Yasunaga, L. Indorf, S. Nestel, S. Lienkamp, H. Omran, W. Kuehn, Olaf Ronneberger, G. Walz, a. Kramer-Zucker

Development, 142(1): 174--184, Jan 2015

U-Net: Convolutional Networks for Biomedical Image Segmentation doi> Code/data

Olaf Ronneberger, Philipp Fischer, Thomas Brox

Medical Image Computing and Computer-Assisted Intervention (MICCAI), Springer, LNCS, Vol.9351: 234--241, 2015

Cell segmentation and tracking in phase contrast images using graph cut with asymmetric boundary costs Paper

doi> Code/data

Robert Bensch, Olaf Ronneberger

IEEE International Symposium on Biomedical Imaging (ISBI): 1220--1223, 2015

Spatiotemporal Deformable Prototypes for Motion Anomaly Detection Paper

doi> Code/data

Robert Bensch, Thomas Brox, Olaf Ronneberger

British Machine Vision Conference (BMVC), BMVA Press: 189.1--189.12, 2015

The iRoCS Toolbox – 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution doi> Code/data

Thorsten Schmidt, T. Pasternak, Kun Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Dürr, W. Teale, F. Ditengou, Hans Burkhardt, Olaf Ronneberger, K. Palme

The Plant Journal, 77(5): 806--814, Mar 2014