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2020

A connectome and analysis of the adult Drosophila central brain.
Scheffer, L.K. and Xu, C.S. and Januszewski, M. and Lu, Z. and Takemura, S. and Hayworth, K.J. and Huang, G.B. and Shinomiya, K. and Maitin-Shepard, J. and Berg, S. and Clements, J. and Hubbard, P. and Katz, W. and Umayam, L. and Zhao, T. and Ackerman, D. and Blakely, T. and Bogovic, J. and Dolafi, T. and Kainmueller, D. and Kawase, T. and Khairy, K.A. and Leavitt, L. and Li, P.H. and Lindsey, L. and Neubarth, N. and Olbris, D.J. and Otsuna, H. and Trautman, E.T. and Ito, M. and Goldammer, J. and Wolff, T. and Svirskas, R. and Schlegel, P. and Neace, E.R. and Knecht, C.J. and Alvarado, C.X. and Bailey, D.A. and Ballinger, S. and Borycz, J.A and Canino, B.S. and Cheatham, N. and Cook, M. and Dreher, M. and Duclos, O. and Eubanks, B. and Fairbanks, K. and Finley, S. and Forknall, N. and Francis, A. and Hopkins, G.P. and Joyce, E.M. and Kim, S.J. and Kirk, N.A. and Kovalyak, J. and Lauchie, S.A. and Lohff, A. and Maldonado, C. and Manley, E.A. and McLin, S. and Mooney, C. and Ndama, M. and Ogundeyi, O. and Okeoma, N. and Ordish, C. and Padilla, N. and Patrick, C. and Paterson, T. and Phillips, E.E. and Phillips, E.M. and Rampally, N. and Ribeiro, C. and Robertson, M.K. and Rymer, J.T. and Ryan, S.M. and Sammons, M. and Scott, A.K. and Scott, A.L. and Shinomiya, A. and Smith, C. and Smith, K. and Smith, N.L. and Sobeski, M.A. and Suleiman, A. and Swift, J. and Takemura, S. and Talebi, I. and Tarnogorska, D. and Tenshaw, E. and Tokhi, T. and Walsh, J.J. and Yang, T. and Horne, J.A. and Li, F. and Parekh, R. and Rivlin, P.K. and Jayaraman, V. and Ito, K. and Saalfeld, S. and George, R. and Meinertzhagen, I.A. and Rubin, G.M. and Hess, H.F. and Jain, V. and Plaza, S.M.
bioRxiv : 2020.04.07.030213. 9 April 2020

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

A connectome of the adult drosophila central brain.
Xu, C.S. and Januszewski, M. and Lu, Z. and Takemura, S. and Hayworth, K.J. and Huang, G. and Shinomiya, K. and Maitin-Shepard, J. and Ackerman, D. and Berg, S. and Blakely, T. and Bogovic, J. and Clements, J. and Dolafi, T. and Hubbard, P. and Kainmueller, D. and Katz, W. and Kawase, T. and Khairy, K.A. and Leavitt, L. and Li, P.H. and Lindsey, L. and Neubarth, N. and Olbris, D.J. and Otsuna, H. and Troutman, E.T. and Umayam, L. and Zhao, T. and Ito, M. and Goldammer, J. and Wolff, T. and Svirskas, R. and Schlegel, P. and Neace, E.R. and Knecht, C.J. and Alvarado, C.X. and Bailey, D.A. and Ballinger, S. and Borycz, J.A. and Canino, B.S. and Cheatham, N. and Cook, M. and Dreher, M. and Duclos, O. and Eubanks, B. and Fairbanks, K. and Finley, S. and Forknall, N. and Francis, A. and Hopkins, G.P. and Joyce, E.M. and Kim, S.J. and Kirk, N.A. and Kovalyak, J. and Lauchie, S.A. and Lohff, A. and Maldonado, C. and Manley, E.A. and McLin, S. and Mooney, C. and Ndama, M. and Ogundeyi, O. and Okeoma, N. and Ordish, C. and Padilla, N. and Patrick, C. and Paterson, T. and Phillips, E.E. and Phillips, E.M. and Rampally, N. and Ribeiro, C. and Robertson, M.K. and Rymer, J.T. and Ryan, S.M. and Sammons, M. and Scott, A.K. and Scott, A.L. and Shinomiya, A. and Smith, C. and Smith, K. and Smith, N.L. and Sobeski, M.A. and Suleiman, A. and Swift, J. and Takemura, S. and Talebi, I. and Tarnogorska, D. and Tenshaw, E. and Tokhi, T. and Walsh, J.J. and Yang, T. and Horne, J.A. and Li, F. and Parekh, R. and Rivlin, P.K. and Jayaraman, V. and Ito, K. and Saalfeld, S. and George, R. and Meinertzhagen, I. and Rubin, G.M. and Hess, H.F. and Scheffer, L.K. and Jain, V. and Plaza, S.M.
bioRxiv : 2020.01.21.911859. 21 January 2020

2019

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

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

A convex relaxation for multi-graph matching.
Swoboda, P. and Kainmüller, D. and Mokarian, A. and 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

2017

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

A study of Lagrangean decompositions and dual ascent solvers for graph matching.
Swoboda, P. and Rother, C. and Alhaija, H.A. and 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. and Jug, F. and Myers, G. and 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

Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
Dye, N.A. and Popovic, M. and Spannl, S. and Etournay, R. and Kainmueller, D. and Myers, E.W. and Julicher, F. and Eaton, S.
bioRxiv : 140038. 19 May 2017

2016

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

GPU-accelerated level-set segmentation.
Lamas-Rodríguez, J. and Heras, D.B. and Argüello, F. and Kainmueller, D. and 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. and Lombardot, B. and Broaddus, C. and Kainmueller, D. and Jug, F. and Myers, E.W. and Vastenhouw, N.L.
Development 143 (3): 540-546. 1 February 2016

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

2015

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

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

2014

Active graph matching for automatic joint segmentation and annotation of C. elegans.
Kainmueller, D. and Jug, F. and 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. and Pietzsch, T. and Kainmüller, D. and Funke, J. and Kaiser, M. and van Nimwegen, E. and Rother, C. and Myers, G.
Lecture Notes in Computer Science 8677 : 25-36. 2014

2013

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

Partitioning and mapping a fast level-set algorithm on the GPU.
Lamas-Rodriguez, J. and Heras, D.B. and Arguello, F. and 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

2012

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

2011

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

2010

3D reconstruction of the human rib cage from 2D projection images using a statistical shape model.
Dworzak, J. and Lamecker, H. and von Berg, J. and Klinder, T. and Lorenz, C. and Kainmüller, D. and Seim, H. and 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. and Lamecker, H. and Seim, H. and Zachow, S. and Hege, H.C.
Lecture Notes in Computer Science 6361 : 227-234. 2010

2009

An articulated statistical shape model for accurate hip joint segmentation.
Kainmueller, D. and Lamecker, H. and 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

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

A system for unsupervised extraction of orthopedic parameters from CT data.
Seim, H. and Kainmüller, D. and 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. and Kainmueller, D. and Heller, M. and 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 extraction of mandibular nerve and bone from cone-beam CT data.
Kainmueller, D. and Lamecker, H. and Seim, H. and Zinser, M. and Zachow, S.
Lecture Notes in Computer Science 5762 : 76-83. 2009

2008

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

Coupling deformable models for multi-object segmentation.
Kainmueller, D. and Lamecker, H. and 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. and Unterhinninghofen, R. and Ley, S. and Dillmann, R.
Proceedings of SPIE 6914 : 691414. 2008

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