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Article

Validity constraints for data analysis workflows.
Schintke, F. and Belhajjame, K. and De Mecquenem, N. and Frantz, D. and Guarino, V.E. and Hilbrich, M. and Lehmann, F. and Missier, P. and Sattler, R. and Sparka, J.A. and Speckhard, D.T. and Stolte, H. and 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. and Vu, Q.D. and Jahanifar, M. and Weigert, M. and Schmidt, U. and Zhang, W. and Zhang, J. and Yang, S. and Xiang, J. and Wang, X. and Rumberger, J.L. and Baumann, E. and Hirsch, P. and Liu, L. and Hong, C. and Aviles-Rivero, A.I. and Jain, A. and Ahn, H. and Hong, Y. and Azzuni, H. and Xu, M. and Yaqub, M. and Blache, M.C. and Piégu, B. and Vernay, B. and Scherr, T. and Böhland, M. and Löffler, K. and Li, J. and Ying, W. and Wang, C. and Snead, D. and Raza, S.E.A. and Minhas, F. and Rajpoot, N.M.
Medical Image Analysis 92 : 103047. February 2024

Heat in Germany: Health risks and preventive measures.
Winklmayr, C. and Matthies-Wiesler, F. and Muthers, S. and Buchien, S. and Kuch, B. and 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. and Greenwald, N.F. and Kong, A. and McCaffrey, E.F. and Leow, K.X. and Mrdjen, D. and Cannon, B.J. and Rumberger, J.L. and 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. and Nern, A. and Dorman, Z. and DePasquale, G.M. and Forster, K. and Gibney, T. and Hausenfluck, J.H. and He, Y. and Iyer, N.A. and Jeter, J. and Johnson, L. and Johnston, R.M. and Lee, K. and Melton, B. and Yarbrough, B. and Zugates, C.T. and Clements, Jody and Goina, C. and Otsuna, H. and Rokicki, K. and Svirskas, R.R. and Aso, Y. and Card, G.M. and Dickson, B.J. and Ehrhardt, E. and Goldammer, J. and Ito, M. and Kainmueller, D. and Korff, W. and Mais, L. and Minegishi, R. and Namiki, S. and Rubin, G.M. and Sterne, G.R. and 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. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Kainmueller, D. and Keller, P.J. and 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. and Obermayer, B. and Mache, C. and Fathykova, D. and Kessler, M. and Dökel, S. and Wyler, E. and Baumgardt, M. and Löwa, A. and Hoffmann, K. and Graff, P. and Schulze, J. and Mieth, M. and Hellwig, K. and Demir, Z. and Biere, B. and Brunotte, L. and Mecate-Zambrano, A. and Bushe, J. and Dohmen, M. and Hinze, C. and Elezkurtaj, S. and Tönnies, M. and Bauer, T.T. and Eggeling, S. and Tran, H.L. and Schneider, P. and Neudecker, J. and Rückert, J.C. and Schmidt-Ott, K.M. and Busch, J. and Klauschen, F. and Horst, D. and Radbruch, H. and Radke, J. and Heppner, F. and Corman, V.M. and Niemeyer, D. and Müller, M.A. and Goffinet, C. and Mothes, R. and Pascual-Reguant, A. and Hauser, A.E. and Beule, D. and Landthaler, M. and Ludwig, S. and Suttorp, N. and Witzenrath, M. and Gruber, A.D. and Drosten, C. and Sander, L.E. and Wolff, T. and 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. and Malin-Mayor, C. and Santella, A. and Preibisch, S. and 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. and Feineis, L. and Hutschenreiter, L. and Bernard, F. and Rother, C. and Kainmüller, D. and 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. and Koch, A. and Guarino, V.E. and Kainmueller, D. and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

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

Probabilistic deep learning for instance segmentation.
Rumberger, J.L. and 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. and Bolondi, A. and Kretzmer, H. and Haut, L. and Scholze-Wittler, M. and Schifferl, D. and Koch, F. and Guignard, L. and Kumar, A.S. and Pustet, M. and Heimann, S. and Buschow, R. and Wittler, L. and Timmermann, B. and Meissner, A. and Herrmann, B.G.
Science 370 (6522): eaba4937. 11 December 2020

PatchPerPix for instance segmentation.
Mais, L. and 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. and Xu, C.S. and Januszewski, M. and Lu, Z. and Takemura, S.Y. and Hayworth, K.J. and Huang, G.B. and Shinomiya, K. and Maitlin-Shepard, J. and Berg, S. and Clements, J. and Hubbard, P.M. and Katz, W.T. 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 Bates, A.S. 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 Costa, M. and Jefferis, G.S.X.E. 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.
eLife 9 : e57443. 7 September 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

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

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

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

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

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

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

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

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

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

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

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

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

Book Section

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P. and 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

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L. and Franzen, J. and Hirsch, P. and 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. and Mohammadi, S. and 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. and Baumann, E. and Hirsch, P. and Janowczyk, A. and 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. and Haller, S. and Feineis, L. and Rother, C. and 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. and Yu, X. and Hirsch, P. and Dohmen, M. and Guarino, V.E. and Mokarian, A. and Mais, L. and 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. 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

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

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

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

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

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

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 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

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. and Reinke, A. and Godau, P. and Tizabi, M.D. and Buettner, F. and Christodoulou, E. and Glocker, B. and Isensee, F. and Kleesiek, J. and Kozubek, M. and Reyes, M. and Riegler, M.A. and Wiesenfarth, M. and Kavur, A.E. and Sudre, C.H. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Rädsch, T. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Blaschko, M.B. and Cardoso, M.J. and Cheplygina, V. and Cimini, B.A. and Collins, G.S. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Haase, R. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Karthikesalingam, A. and Kofler, F. and Kopp-Schneider, A. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Mattson, P. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rajpoot, N. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and van Smeden, M. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and 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. and Tizabi, M.D. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Kavur, A.E. and Rädsch, T. and Sudre, C.H. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Buettner, F. and Cardoso, M.J. and Cheplygina, V. and Chen, J. and Christodoulou, E. and Cimini, B.A. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Glocker, B. and Godau, P. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Isensee, F. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Kleesiek, J. and Kofler, F. and Kooi, T. and Kopp-Schneider, A. and Kozubek, M. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rafelski, S.M. and Rajpoot, N. and Reyes, M. and Riegler, M.A. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and Varoquaux, G. and Yaniv, Z.R. and 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. and Weidenfeld, S. and Grimmer, B. and Fatykhova, D. and Solymosi, P.D. and Behrens, F. and Dohmen, M. and Brack, M.C. and Schulz, S. and Thomasch, E. and Simmons, S. and Müller-Redetzky, H. and Suttorp, N. and Kurth, F. and Neudecker, J. and Toennies, M. and Bauer, T.T. and Eggeling, S. and Corman, V.M. and Hocke, A.C. and Witzenrath, M. and Hippenstiel, S. and Kuebler, W.M.
European Respiratory Journal 57 (3): 2002384. 11 March 2021

Preprint

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L. and Baumann, E. and Hirsch, P. and Janowczyk, A. and Zlobec, I. and Kainmueller, D.
arXiv : 2203.11692. 19 April 2022

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Keller, P.J. and Preibisch, S. and Funke, J.
bioRxiv : 2021.07.28.454016. 29 July 2021

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

Probabilistic deep learning for instance segmentation.
Rumberger, J.L. and Mais, L. and Kainmueller, D.
arXiv : 2008.10678. 24 August 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

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

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