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Jump to: 2021 IEEE/CVF International Conference on Computer Vision (ICCV) | 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC) | 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW) | 2024 IEEE International Symposium on Biomedical Imaging (ISBI) | 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | 2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW) | Advances in Neural Information Processing Systems | Annals of Oncology | CEUR Workshop Proceedings | Communications Physics | Communications in Computer and Information Science | Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference | Datenbank-Spektrum | Development | European Respiratory Journal | Future Generation Computer Systems | Hugging Face | Human Brain Mapping | IEEE Transactions on Medical Imaging | IEEE Workshop on Applications of Computer Vision (WACV) | Informatik aktuell | International Journal of Computer Assisted Radiology and Surgery | Journal of Health Monitoring | Journal of Pathology Informatics | Journal of Real-Time Image Processing | Lecture Notes in Computer Science | Medical Image Analysis | Nature Biotechnology | Nature Cardiovascular Research | Nature Communications | Nature Methods | Proceedings of Machine Learning Research | Proceedings of SPIE | Proceedings of the British Machine Vision Conference (BMVC) | Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition | Science | Scientific Reports | Zenodo | arXiv | bioRxiv | eLife

2021 IEEE/CVF International Conference on Computer Vision (ICCV)

Fusion moves for graph matching.
Hutschenreiter, L., Haller, S., Feineis, L., Rother, C., Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 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. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Yu, X., Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Dohmen, M. ORCID logoORCID: https://orcid.org/0000-0002-4447-0579, Guarino, V.E. ORCID logoORCID: https://orcid.org/0000-0003-1625-4323, Mokarian, A., Mais, L. ORCID logoORCID: https://orcid.org/0000-0002-9281-2668, Funke, J. and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC)

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Baumann, E., Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Janowczyk, A., Zlobec, I. and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 28-31 March 2022, Kolkata, India. 17 August 2022

2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Franzen, J. ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Albrecht, J.P. ORCID logoORCID: https://orcid.org/0000-0002-3792-9695 and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
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. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 and Hoehne, J.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

2024 IEEE International Symposium on Biomedical Imaging (ISBI)

Simultaneous lung cell and nucleus segmentation from labelled versus unlabelled human lung DIC images.
Dohmen, M. ORCID logoORCID: https://orcid.org/0000-0002-4447-0579, Mittermaier, M., Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Yang, L.L., Gruber, A.D., Toennies, M., Hippenstiel, S., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 and Hocke, A.C.
In: 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 27-30 May 2024, Athens, Greece. 22 August 2024

2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

FISBe: a real-world benchmark dataset for instance segmentation of long-range thin filamentous structures.
Mais, L. ORCID logoORCID: https://orcid.org/0000-0002-9281-2668, Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Managan, Claire, Kandarpa, Ramya, Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Reinke, Annika, Maier-Hein, Lena, Ihrke, Gudrun and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 16-22 June 2024, Seattle, WA, USA. 16 September 2024

2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)

SelfAdapt: unsupervised domain adaptation of cell segmentation models.
Reith, Fabian H. ORCID logoORCID: https://orcid.org/0000-0002-0745-2726, Franzen, Jannik ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Rumberger, J. Lorenz ORCID logoORCID: https://orcid.org/0000-0002-7225-7011 and Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 19-20 Oct 2025, Honolulu, HI, USA. 23 February 2026

Advances in Neural Information Processing Systems

Arctique: an artificial histopathological dataset unifying realism and controllability for uncertainty quantification.
Franzen, J. ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Winklmayr, C. ORCID logoORCID: https://orcid.org/0000-0002-8784-2301, Guarino, V.E. ORCID logoORCID: https://orcid.org/0000-0003-1625-4323, Karg, C., Yu, X., Koreuber, N. ORCID logoORCID: https://orcid.org/0009-0003-9328-4590, Albrecht, J.P. ORCID logoORCID: https://orcid.org/0000-0002-3792-9695, Bischoff, P. and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 38th Conference on Neural Information Processing Systems, NeurIPS 2024, 09-15 Dec 2024, Vancouver, BC, Canada. February 2025

Annals of Oncology

PET/CT-guided management of immune checkpoint blockade and multi-modal profiling following treatment in long-term responders with metastatic lung cancer in the National Network Genomic Medicine Lung Cancer Germany (nNGM).
Frost, N. ORCID logoORCID: https://orcid.org/0000-0001-7452-7129, Joosten, M., Franzen, J. ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Wiesweg, M. ORCID logoORCID: https://orcid.org/0000-0002-9698-9559, Rasokat, A., Kulhavy, J., Kollmeier, J., Reinmuth, N., Grohé, C., Roeper, J., Rittmeyer, A. ORCID logoORCID: https://orcid.org/0000-0002-5280-6052, Heinzen, S., Wermke, M. ORCID logoORCID: https://orcid.org/0000-0002-4844-4087, Wesseler, C. ORCID logoORCID: https://orcid.org/0000-0002-9261-7504, Christopoulos, P. ORCID logoORCID: https://orcid.org/0000-0002-7966-8980, Kauffmann-Guerrero, D., Althoff, A., Bleckmann, A., Collienne, M. ORCID logoORCID: https://orcid.org/0000-0003-0932-2471, Berezucki, E., Overbeck, T. ORCID logoORCID: https://orcid.org/0000-0002-2579-0171, Kropf-Sanchen, C., Griesinger, F., Sebastian, M. ORCID logoORCID: https://orcid.org/0000-0002-0404-7741, Schuler, M. ORCID logoORCID: https://orcid.org/0000-0002-2166-3394, Braun, S., Wenzel, C., Furth, C. ORCID logoORCID: https://orcid.org/0000-0001-7302-7886, Wolf, J., Bischoff, P. ORCID logoORCID: https://orcid.org/0000-0002-4442-7116 and Reck, M. ORCID logoORCID: https://orcid.org/0000-0002-5348-4462
Annals of Oncology 37 (5): 686-700. May 2026

CEUR Workshop Proceedings

TLIMB - a transfer learning framework for image analysis of the brain.
Schulz, M.A., Albrecht, J.P. ORCID logoORCID: https://orcid.org/0000-0002-3792-9695, Yilmaz, A., Koch, A., Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

Communications Physics

Artificial-intelligence-driven scanning probe microscopy.
Krull, A., Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Rother, C., Schiffrin, A. ORCID logoORCID: https://orcid.org/0000-0003-1140-8485 and Krull, C.
Communications Physics 3 (1): 54. 19 March 2020

Communications in Computer and Information Science

Model guidance via explanations turns image classifiers into segmentation models.
Yu, X. ORCID logoORCID: https://orcid.org/0000-0001-8196-663X, Franzen, J. ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Samek, W. ORCID logoORCID: https://orcid.org/0000-0002-6283-3265, Höhne, M.M.C. ORCID logoORCID: https://orcid.org/0000-0003-3090-6279 and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: Second World Conference, xAI 2024, July 17–19, 2024, Valletta, Malta. 10 July 2024

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

An articulated statistical shape model for accurate hip joint segmentation.
Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

Datenbank-Spektrum

The Collaborative Research Center FONDA.
Leser, U., Hilbrich, M., Draxl, C., Eisert, P., Grunske, L., Hostert, P., Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

Development

Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
Dye, N.A. ORCID logoORCID: https://orcid.org/0000-0002-4859-6670, Popović, M. ORCID logoORCID: https://orcid.org/0000-0003-2360-3982, Spannl, S., Etournay, R. ORCID logoORCID: https://orcid.org/0000-0002-2441-9274, Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Ghosh, S., Myers, E.W. ORCID logoORCID: https://orcid.org/0000-0002-6580-7839, Jülicher, F. ORCID logoORCID: https://orcid.org/0000-0003-4731-9185 and Eaton, S.
Development 144 (23): 4406-4421. 1 December 2017

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
Stapel, L.C. ORCID logoORCID: https://orcid.org/0000-0003-0808-5005, Lombardot, B., Broaddus, C., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Jug, F., Myers, E.W. and Vastenhouw, N.L.
Development 143 (3): 540-546. 1 February 2016

European Respiratory Journal

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. ORCID logoORCID: https://orcid.org/0000-0002-9116-630X, Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E. ORCID logoORCID: https://orcid.org/0000-0002-9884-1806, Baumgardt, M., Löwa, A. ORCID logoORCID: https://orcid.org/0000-0002-5551-731X, Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M. ORCID logoORCID: https://orcid.org/0000-0002-4447-0579, Hinze, C. ORCID logoORCID: https://orcid.org/0000-0003-2526-1621, Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M. ORCID logoORCID: https://orcid.org/0000-0002-7700-7142, Busch, J., Klauschen, F., Horst, D., Radbruch, H. ORCID logoORCID: https://orcid.org/0000-0001-6941-3397, Radke, J., Heppner, F., Corman, V.M., Niemeyer, D. ORCID logoORCID: https://orcid.org/0000-0002-1897-6365, Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D. ORCID logoORCID: https://orcid.org/0000-0002-3284-0632, Landthaler, M. ORCID logoORCID: https://orcid.org/0000-0002-1075-8734, 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

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. ORCID logoORCID: https://orcid.org/0000-0002-6841-4192, Dohmen, M. ORCID logoORCID: https://orcid.org/0000-0002-4447-0579, Brack, M.C., Schulz, S., Thomasch, E., Simmons, S., Müller-Redetzky, H., Suttorp, N., Kurth, F. ORCID logoORCID: https://orcid.org/0000-0002-3807-473X, 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

Future Generation Computer Systems

Validity constraints for data analysis workflows.
Schintke, F., Belhajjame, K., De Mecquenem, N., Frantz, D., Guarino, V.E. ORCID logoORCID: https://orcid.org/0000-0003-1625-4323, 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

Hugging Face

PathoCell: a benchmark for foundational models in computational pathology.
Reith, F.H. ORCID logoORCID: https://orcid.org/0000-0002-0745-2726
[Dataset] September 2025

Pan-Multiplex (Pan-M) dataset.
Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011
[Dataset] May 2025 (Submitted)

Human Brain Mapping

Do transformers and CNNs learn different concepts of brain age?
Siegel, N.T. ORCID logoORCID: https://orcid.org/0009-0008-2385-1656, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Deniz, F., Ritter, K. and Schulz, M.A.
Human Brain Mapping 46 (8): e70243. 1 June 2025

IEEE Transactions on Medical Imaging

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. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

IEEE Workshop on Applications of Computer Vision (WACV)

Cycle-consistent multi-graph matching for self-supervised annotation of C.Elegans.
Stricker, Sebastian, Karg, Christoph, Hutschenreiter, Lisa, Savchynskyy, Bogdan and Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: 2026 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 06-10 Mar 2026, Tucson, AZ, USA. 6 March 2026

Informatik aktuell

An articulated statistical shape model of the human knee.
Bindernagel, M., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Seim, H., Lamecker, H., Zachow, S. and Hege, H.C.
Informatik aktuell : 59-63. 2011

International Journal of Computer Assisted Radiology and Surgery

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. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Seim, H., Hege, H.C. and Zachow, S.
International Journal of Computer Assisted Radiology and Surgery 5 (2): 111-124. March 2010

Journal of Health Monitoring

Heat in Germany: Health risks and preventive measures.
Winklmayr, C. ORCID logoORCID: https://orcid.org/0000-0002-8784-2301, 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

Journal of Pathology Informatics

PD-L1 expression assessment in Angiosarcoma improves with artificial intelligence support.
Reith, F.H. ORCID logoORCID: https://orcid.org/0000-0002-0745-2726, Jarosch, A., Albrecht, J.P. ORCID logoORCID: https://orcid.org/0000-0002-3792-9695, Ghoreschi, F., Flörcken, A., Dörr, A., Roohani, S., Schäfer, F.M., Öllinger, R., Märdian, S., Tielking, K., Bischoff, P., Frühauf, N., Brandes, F., Horst, D., Sers, C. and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
Journal of Pathology Informatics 18 : 100447. August 2025

Journal of Real-Time Image Processing

GPU-accelerated level-set segmentation.
Lamas-Rodríguez, J., Heras, D.B., Argüello, F., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Zachow, S. and Bóo, M.
Journal of Real-Time Image Processing 12 (1): 15-29. June 2016

Lecture Notes in Computer Science

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

Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Malin-Mayor, C. ORCID logoORCID: https://orcid.org/0000-0002-9627-6030, Santella, A., Preibisch, S. ORCID logoORCID: https://orcid.org/0000-0002-0276-494X, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 and Funke, J. ORCID logoORCID: 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 logoORCID: https://orcid.org/0000-0002-0855-8549, Feineis, L., Hutschenreiter, L., Bernard, F., Rother, C., Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Swoboda, P. ORCID logoORCID: 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 logoORCID: https://orcid.org/0000-0003-1625-4323, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

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

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

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

Uncertainty-driven forest predictors for vertebra localization and segmentation.
Richmond, D., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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. ORCID logoORCID: 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

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

Improving deformable surface meshes through omni-directional displacements and MRFs.
Kainmueller, D. ORCID logoORCID: 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

Automatic extraction of mandibular nerve and bone from cone-beam CT data.
Kainmueller, D. ORCID logoORCID: 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

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

Medical Image Analysis

CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting.
Graham, S. ORCID logoORCID: https://orcid.org/0000-0002-2214-8212, Vu, Q.D., Jahanifar, M., Weigert, M. ORCID logoORCID: https://orcid.org/0000-0002-7780-9057, Schmidt, U., Zhang, W., Zhang, J. ORCID logoORCID: https://orcid.org/0000-0001-5579-7094, Yang, S., Xiang, J., Wang, X. ORCID logoORCID: https://orcid.org/0000-0002-3597-9090, Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Baumann, E., Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Liu, L. ORCID logoORCID: https://orcid.org/0000-0002-8983-2342, Hong, C., Aviles-Rivero, A.I., Jain, A., Ahn, H., Hong, Y., Azzuni, H. ORCID logoORCID: https://orcid.org/0000-0001-7267-8919, Xu, M., Yaqub, M. ORCID logoORCID: https://orcid.org/0000-0001-6896-1105, Blache, M.C., Piégu, B., Vernay, B. ORCID logoORCID: https://orcid.org/0000-0002-7843-3872, Scherr, T. ORCID logoORCID: https://orcid.org/0000-0001-8755-2825, Böhland, M. ORCID logoORCID: https://orcid.org/0000-0002-9321-8169, Löffler, K. ORCID logoORCID: https://orcid.org/0000-0001-9769-3517, Li, J., Ying, W., Wang, C., Snead, D., Raza, S.E.A. ORCID logoORCID: https://orcid.org/0000-0002-1097-1738, Minhas, F. and Rajpoot, N.M. ORCID logoORCID: https://orcid.org/0000-0002-4706-1308
Medical Image Analysis 92 : 103047. February 2024

Omnidirectional displacements for deformable surfaces.
Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Lamecker, H., Heller, M.O. ORCID logoORCID: https://orcid.org/0000-0002-7879-1135, Weber, B., Hege, H.C. and Zachow, S.
Medical Image Analysis 17 (4): 429-441. May 2013

Nature Biotechnology

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C., Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Guignard, L. ORCID logoORCID: https://orcid.org/0000-0002-3686-1385, McDole, K., Wan, Y., Lemon, W.C. ORCID logoORCID: https://orcid.org/0000-0003-4541-738X, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Keller, P.J. ORCID logoORCID: https://orcid.org/0000-0003-2896-4920, Preibisch, S. ORCID logoORCID: https://orcid.org/0000-0002-0276-494X and Funke, J. ORCID logoORCID: https://orcid.org/0000-0003-4388-7783
Nature Biotechnology 44 (1): 44-49. January 2023

Nature Cardiovascular Research

Mechanosensitive PIEZO2 channels shape coronary artery development.
Pampols-Perez, M. ORCID logoORCID: https://orcid.org/0009-0008-1619-204X, Fürst, C., Sánchez-Carranza, O. ORCID logoORCID: https://orcid.org/0000-0002-8745-5176, Cano, E. ORCID logoORCID: https://orcid.org/0000-0003-1091-8934, Garcia-Contreras, J.A., Mais, L. ORCID logoORCID: https://orcid.org/0000-0002-9281-2668, Luo, W. ORCID logoORCID: https://orcid.org/0000-0001-5202-8855, Raimundo, S. ORCID logoORCID: https://orcid.org/0009-0000-3353-5456, Lindberg, E.L. ORCID logoORCID: https://orcid.org/0000-0002-2979-433X, Taube, M., Heuser, A. ORCID logoORCID: https://orcid.org/0000-0002-3334-960X, Sporbert, A. ORCID logoORCID: https://orcid.org/0000-0002-3738-1295, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Bernabeu, M.O., Hübner, N. ORCID logoORCID: https://orcid.org/0000-0002-1218-6223, Gerhardt, H. ORCID logoORCID: https://orcid.org/0000-0002-3030-0384, Lewin, G.R. ORCID logoORCID: https://orcid.org/0000-0002-2890-6352 and Hammes, A. ORCID logoORCID: https://orcid.org/0000-0003-1663-8378
Nature Cardiovascular Research 4 (7): 921-937. July 2025

Nature Communications

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering.
Liu, C.C., Greenwald, N.F. ORCID logoORCID: https://orcid.org/0000-0002-7836-4379, Kong, A., McCaffrey, E.F., Leow, K.X., Mrdjen, D., Cannon, B.J. ORCID logoORCID: https://orcid.org/0000-0003-4418-1803, Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Varra, S.R. ORCID logoORCID: https://orcid.org/0009-0000-5757-6818 and Angelo, M. ORCID logoORCID: https://orcid.org/0000-0003-1531-5067
Nature Communications 14 (1): 4618. 1 August 2023

Nature Methods

Automated classification of cellular expression in multiplexed imaging data with Nimbus.
Rumberger, Josef Lorenz ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Greenwald, Noah F. ORCID logoORCID: https://orcid.org/0000-0002-7836-4379, Ranek, Jolene S., Boonrat, Potchara, Walker, Cameron, Franzen, Jannik ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Varra, Sricharan Reddy ORCID logoORCID: https://orcid.org/0009-0000-5757-6818, Kong, Alex, Sowers, Cameron, Liu, Candace C., Averbukh, Inna, Piyadasa, Hadeesha, Vanguri, Rami, Nederlof, Iris ORCID logoORCID: https://orcid.org/0000-0001-7608-6515, Wang, Xuefei Julie ORCID logoORCID: https://orcid.org/0000-0002-9327-9543, Van Valen, David ORCID logoORCID: https://orcid.org/0000-0001-7534-7621, Kok, Marleen, Bendall, Sean C. ORCID logoORCID: https://orcid.org/0000-0003-1341-2453, Hollmann, Travis J., Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415 and Angelo, Michael ORCID logoORCID: https://orcid.org/0000-0003-1531-5067
Nature Methods 22 (10): 2161-2170. October 2025

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L. ORCID logoORCID: https://orcid.org/0000-0003-4910-9368, Reinke, A. ORCID logoORCID: https://orcid.org/0000-0003-4363-1876, Godau, P. ORCID logoORCID: https://orcid.org/0000-0002-0365-7265, Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B. ORCID logoORCID: https://orcid.org/0000-0002-4897-9356, Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A. ORCID logoORCID: https://orcid.org/0000-0002-3153-2064, Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M. ORCID logoORCID: https://orcid.org/0000-0002-0713-8761, Heckmann-Nötzel, D., Rädsch, T. ORCID logoORCID: https://orcid.org/0000-0003-3518-0315, Acion, L. ORCID logoORCID: https://orcid.org/0000-0001-5213-6012, Antonelli, M. ORCID logoORCID: https://orcid.org/0000-0002-3005-4523, Arbel, T. ORCID logoORCID: https://orcid.org/0000-0001-8870-3007, Bakas, S. ORCID logoORCID: https://orcid.org/0000-0001-8734-6482, Benis, A. ORCID logoORCID: https://orcid.org/0000-0002-9125-8300, Blaschko, M.B., Cardoso, M.J. ORCID logoORCID: https://orcid.org/0000-0003-1284-2558, Cheplygina, V. ORCID logoORCID: https://orcid.org/0000-0003-0176-9324, Cimini, B.A. ORCID logoORCID: https://orcid.org/0000-0001-9640-9318, Collins, G.S. ORCID logoORCID: https://orcid.org/0000-0002-2772-2316, Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Haase, R. ORCID logoORCID: https://orcid.org/0000-0001-5949-2327, Hashimoto, D.A. ORCID logoORCID: https://orcid.org/0000-0003-4725-3104, Hoffman, M.M. ORCID logoORCID: https://orcid.org/0000-0002-4517-1562, Huisman, M., Jannin, P. ORCID logoORCID: https://orcid.org/0000-0002-7415-071X, Kahn, C.E. ORCID logoORCID: https://orcid.org/0000-0002-6654-7434, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Kainz, B., Karargyris, A. ORCID logoORCID: https://orcid.org/0000-0002-1930-3410, Karthikesalingam, A., Kofler, F., Kopp-Schneider, A. ORCID logoORCID: https://orcid.org/0000-0002-1810-0267, Kreshuk, A. ORCID logoORCID: https://orcid.org/0000-0003-1334-6388, Kurc, T., Landman, B.A. ORCID logoORCID: https://orcid.org/0000-0001-5733-2127, Litjens, G. ORCID logoORCID: https://orcid.org/0000-0003-1554-1291, Madani, A., Maier-Hein, K., Martel, A.L. ORCID logoORCID: https://orcid.org/0000-0003-1375-5501, Mattson, P. ORCID logoORCID: https://orcid.org/0000-0002-5984-238X, Meijering, E. ORCID logoORCID: https://orcid.org/0000-0001-8015-8358, Menze, B. ORCID logoORCID: https://orcid.org/0000-0003-4136-5690, Moons, K.G.M., Müller, H. ORCID logoORCID: https://orcid.org/0000-0001-6800-9878, Nichyporuk, B. ORCID logoORCID: https://orcid.org/0009-0006-8087-6089, Nickel, F., Petersen, J., Rajpoot, N. ORCID logoORCID: https://orcid.org/0000-0002-4706-1308, Rieke, N. ORCID logoORCID: https://orcid.org/0000-0003-0241-9334, Saez-Rodriguez, J. ORCID logoORCID: https://orcid.org/0000-0002-8552-8976, Sánchez, C.I., Shetty, S., van Smeden, M., Summers, R.M. ORCID logoORCID: https://orcid.org/0000-0001-8081-7376, Taha, A.A. ORCID logoORCID: https://orcid.org/0000-0002-7604-9041, Tiulpin, A. ORCID logoORCID: https://orcid.org/0000-0002-7852-4141, Tsaftaris, S.A., Van Calster, B., Varoquaux, G. ORCID logoORCID: https://orcid.org/0000-0003-1076-5122 and Jäger, P.F. ORCID logoORCID: https://orcid.org/0000-0002-6243-2568
Nature Methods 21 (2): 195-212. 12 February 2024

Understanding metric-related pitfalls in image analysis validation.
Reinke, A. ORCID logoORCID: https://orcid.org/0000-0003-4363-1876, Tizabi, M.D. ORCID logoORCID: https://orcid.org/0000-0003-3687-6381, Baumgartner, M. ORCID logoORCID: https://orcid.org/0000-0003-4455-9917, Eisenmann, M., Heckmann-Nötzel, D., Kavur, A.E. ORCID logoORCID: https://orcid.org/0000-0002-9328-8140, Rädsch, T. ORCID logoORCID: https://orcid.org/0000-0003-3518-0315, Sudre, C.H., Acion, L. ORCID logoORCID: https://orcid.org/0000-0001-5213-6012, Antonelli, M. ORCID logoORCID: https://orcid.org/0000-0002-3005-4523, Arbel, T., Bakas, S. ORCID logoORCID: https://orcid.org/0000-0001-8734-6482, Benis, A. ORCID logoORCID: https://orcid.org/0000-0002-9125-8300, Buettner, F., Cardoso, M.J. ORCID logoORCID: https://orcid.org/0000-0003-1284-2558, Cheplygina, V. ORCID logoORCID: https://orcid.org/0000-0003-0176-9324, Chen, J. ORCID logoORCID: https://orcid.org/0000-0002-8500-1357, Christodoulou, E., Cimini, B.A. ORCID logoORCID: https://orcid.org/0000-0001-9640-9318, Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Glocker, B. ORCID logoORCID: https://orcid.org/0000-0002-4897-9356, Godau, P. ORCID logoORCID: https://orcid.org/0000-0002-0365-7265, Hashimoto, D.A. ORCID logoORCID: https://orcid.org/0000-0003-4725-3104, Hoffman, M.M. ORCID logoORCID: https://orcid.org/0000-0002-4517-1562, Huisman, M., Isensee, F., Jannin, P. ORCID logoORCID: https://orcid.org/0000-0002-7415-071X, Kahn, C.E. ORCID logoORCID: https://orcid.org/0000-0002-6654-7434, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Kainz, B., Karargyris, A. ORCID logoORCID: https://orcid.org/0000-0002-1930-3410, Kleesiek, J. ORCID logoORCID: https://orcid.org/0000-0001-8686-0682, Kofler, F., Kooi, T., Kopp-Schneider, A. ORCID logoORCID: https://orcid.org/0000-0002-1810-0267, Kozubek, M. ORCID logoORCID: https://orcid.org/0000-0001-7902-589X, Kreshuk, A. ORCID logoORCID: https://orcid.org/0000-0003-1334-6388, Kurc, T., Landman, B.A. ORCID logoORCID: https://orcid.org/0000-0001-5733-2127, Litjens, G. ORCID logoORCID: https://orcid.org/0000-0003-1554-1291, Madani, A., Maier-Hein, K., Martel, A.L. ORCID logoORCID: https://orcid.org/0000-0003-1375-5501, Meijering, E. ORCID logoORCID: https://orcid.org/0000-0001-8015-8358, Menze, B. ORCID logoORCID: https://orcid.org/0000-0003-4136-5690, Moons, K.G.M., Müller, H. ORCID logoORCID: https://orcid.org/0000-0001-6800-9878, Nichyporuk, B. ORCID logoORCID: https://orcid.org/0009-0006-8087-6089, Nickel, F., Petersen, J., Rafelski, S.M. ORCID logoORCID: https://orcid.org/0000-0002-1399-5970, Rajpoot, N. ORCID logoORCID: https://orcid.org/0000-0002-4706-1308, Reyes, M., Riegler, M.A. ORCID logoORCID: https://orcid.org/0000-0002-3153-2064, Rieke, N. ORCID logoORCID: https://orcid.org/0000-0003-0241-9334, Saez-Rodriguez, J. ORCID logoORCID: https://orcid.org/0000-0002-8552-8976, Sánchez, C.I., Shetty, S., Summers, R.M. ORCID logoORCID: https://orcid.org/0000-0001-8081-7376, Taha, A.A., Tiulpin, A. ORCID logoORCID: https://orcid.org/0000-0002-7852-4141, Tsaftaris, S.A., Van Calster, B., Varoquaux, G. ORCID logoORCID: https://orcid.org/0000-0003-1076-5122, Yaniv, Z.R. ORCID logoORCID: https://orcid.org/0000-0003-0315-7727, Jäger, P.F. ORCID logoORCID: https://orcid.org/0000-0002-6243-2568 and Maier-Hein, L. ORCID logoORCID: https://orcid.org/0000-0003-4910-9368
Nature Methods 21 (2): 182-194. February 2024

Proceedings of Machine Learning Research

HoVer-NeXt: a fast nuclei segmentation and classification pipeline for next generation histopathology.
Baumann, E., Dislich, B., Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Nagtegaal, I.D., Martínez, M.R. and Zlobec, I.
In: 7th International Conference on Medical Imaging with Deep Learning, 03-05 Jul 2024, Paris, France. 2024

An auxiliary task for learning nuclei segmentation in 3D microscopy images.
Hirsch, Peter ORCID logoORCID: https://orcid.org/0000-0002-2353-5310 and Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
In: Third Conference on Medical Imaging with Deep Learning, 6-8 Jul 2020, Montreal, QC, Canada. 2020

Proceedings of SPIE

Level set segmentation of the heart from 4D phase contrast MRI.
Kainmuller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Unterhinninghofen, R., Ley, S. and Dillmann, R.
Proceedings of SPIE 6914 : 691414. 2008

Proceedings of the British Machine Vision Conference (BMVC)

Mapping auto-context decision forests to deep ConvNets for semantic segmentation.
Richmond, D., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Yang, M., Myers, E. and Rother, C.
In: 27th British Machine Vision Conference, BMVC 2016, 19-22 Sep 2016, York, United Kingdom. September 2016

Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition

A convex relaxation for multi-graph matching.
Swoboda, P., Kainmüller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

Science

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites.
Veenvliet, J.V. ORCID logoORCID: https://orcid.org/0000-0002-1191-2975, Bolondi, A. ORCID logoORCID: https://orcid.org/0000-0002-1096-9435, Kretzmer, H. ORCID logoORCID: https://orcid.org/0000-0002-0723-4980, Haut, L., Scholze-Wittler, M., Schifferl, D. ORCID logoORCID: https://orcid.org/0000-0003-3507-5734, Koch, F., Guignard, L. ORCID logoORCID: https://orcid.org/0000-0002-3686-1385, Kumar, A.S., Pustet, M., Heimann, S. ORCID logoORCID: https://orcid.org/0000-0001-8647-1644, Buschow, R. ORCID logoORCID: https://orcid.org/0000-0002-9800-2578, Wittler, L., Timmermann, B., Meissner, A. ORCID logoORCID: https://orcid.org/0000-0001-8646-7469 and Herrmann, B.G. ORCID logoORCID: https://orcid.org/0000-0002-2192-8188
Science 370 (6522): eaba4937. 11 December 2020

Scientific Reports

Content-based image retrieval assists radiologists in diagnosing eye and orbital mass lesions in MRI.
Rumberger, J.L. ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Lim, W., Wildfeuer, B., Sodemann, E.B., Lecler, A., Stemplinger, S., Issever, A.S., Sepahdari, A., Langner, S., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Hamm, B. and Erb-Eigner, K.
Scientific Reports 15 (1): 11334. 2 April 2025

The cell adhesion protein CAR is a negative regulator of synaptic transmission.
Wrackmeyer, U., Kaldrack, J., Jüttner, R. ORCID logoORCID: https://orcid.org/0000-0003-3565-0698, Pannasch, U. ORCID logoORCID: https://orcid.org/0000-0001-6502-1046, Gimber, N. ORCID logoORCID: https://orcid.org/0000-0001-9456-3063, Freiberg, F., Purfürst, B. ORCID logoORCID: https://orcid.org/0000-0002-9887-7577, Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Schmitz, D. ORCID logoORCID: https://orcid.org/0000-0003-2741-5241, Haucke, V. ORCID logoORCID: https://orcid.org/0000-0003-3119-6993, Rathjen, F.G. ORCID logoORCID: https://orcid.org/0000-0001-5351-613X and Gotthardt, M. ORCID logoORCID: https://orcid.org/0000-0003-1788-3172
Scientific Reports 9 (1): 6768. 1 May 2019

Zenodo

PET/CT-guided management of immune checkpoint blockade and post-treatment multi-modal profiling in long-term responders with metastatic lung cancer in the National Network Genomic Medicine Lung Cancer Germany (nNGM).
Bischoff, Philip and Franzen, Jannik ORCID logoORCID: https://orcid.org/0000-0002-0761-641X
[Dataset] 4 December 2025

arXiv

Vesselpose: vessel graph reconstruction from learned voxel-wise direction vectors in 3D vascular images.
Palaniappan, Rajalakshmi, Karg, Christoph, Navarro-Arambula, Nemesio, Hirsch, Peter ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Kraeker, Kristin ORCID logoORCID: https://orcid.org/0000-0002-4032-5382, Mais, Lisa ORCID logoORCID: https://orcid.org/0000-0002-9281-2668 and Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
arXiv : 2605.00538v1. 1 May 2026

Better than average: spatially-aware aggregation of segmentation uncertainty improves downstream performance.
Guarino, Vanessa Emanuela ORCID logoORCID: https://orcid.org/0000-0003-1625-4323, Winklmayr, Claudia ORCID logoORCID: https://orcid.org/0000-0002-8784-2301, Franzen, Jannik ORCID logoORCID: https://orcid.org/0000-0002-0761-641X, Rumberger, Josef Lorenz ORCID logoORCID: https://orcid.org/0000-0002-7225-7011, Pfeuffer, Manuel, Greven, Sonja, Maier-Hein, Klaus, Lüth, Carsten T., Karg, Christoph and Kainmueller, Dagmar ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
arXiv : 2603.29941. 31 March 2026

ARI3D: a software for interactive quantification of regions in X-ray CT 3D images.
Albrecht, Jan Phillipp ORCID logoORCID: https://orcid.org/0000-0002-3792-9695, Godinho, Jose R.A., Hübers, Christina and Schmidt, Deborah ORCID logoORCID: https://orcid.org/0000-0002-8621-9438
arXiv : 2508.09849. 13 August 2025

bioRxiv

PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L. ORCID logoORCID: https://orcid.org/0000-0002-9281-2668, Hirsch, P. ORCID logoORCID: https://orcid.org/0000-0002-2353-5310, Managan, C. ORCID logoORCID: https://orcid.org/0000-0002-9510-6443, Wang, K., Rokicki, K. ORCID logoORCID: https://orcid.org/0000-0002-2799-9833, Svirskas, R.R. ORCID logoORCID: https://orcid.org/0000-0001-8374-6008, Dickson, B.J. ORCID logoORCID: https://orcid.org/0000-0003-0715-892X, Korff, W. ORCID logoORCID: https://orcid.org/0000-0001-8396-1533, Rubin, G.M. ORCID logoORCID: https://orcid.org/0000-0001-8762-8703, Ihrke, G. ORCID logoORCID: https://orcid.org/0000-0003-4604-735X, Meissner, G.W. ORCID logoORCID: https://orcid.org/0000-0003-0369-9788 and Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415
bioRxiv : 2021.07.23.453511. 26 July 2021

eLife

A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
Meissner, G.W. ORCID logoORCID: https://orcid.org/0000-0003-0369-9788, Nern, A. ORCID logoORCID: https://orcid.org/0000-0002-3822-489X, Dorman, Z. ORCID logoORCID: https://orcid.org/0000-0001-9933-7217, DePasquale, G.M., Forster, K., Gibney, T. ORCID logoORCID: https://orcid.org/0000-0001-5461-724X, Hausenfluck, J.H., He, Y., Iyer, N.A., Jeter, J., Johnson, L., Johnston, R.M., Lee, K., Melton, B., Yarbrough, B., Zugates, C.T. ORCID logoORCID: https://orcid.org/0000-0003-1882-3665, Clements, Jody ORCID logoORCID: https://orcid.org/0000-0003-3932-8188, Goina, C. ORCID logoORCID: https://orcid.org/0000-0003-2835-7602, Otsuna, H. ORCID logoORCID: https://orcid.org/0000-0002-2107-8881, Rokicki, K. ORCID logoORCID: https://orcid.org/0000-0002-2799-9833, Svirskas, R.R. ORCID logoORCID: https://orcid.org/0000-0001-8374-6008, Aso, Y., Card, G.M., Dickson, B.J. ORCID logoORCID: https://orcid.org/0000-0003-0715-892X, Ehrhardt, E. ORCID logoORCID: https://orcid.org/0000-0002-9252-1414, Goldammer, J. ORCID logoORCID: https://orcid.org/0000-0002-5623-8339, Ito, M., Kainmueller, D. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, Korff, W. ORCID logoORCID: https://orcid.org/0000-0001-8396-1533, Mais, L. ORCID logoORCID: https://orcid.org/0000-0002-9281-2668, Minegishi, R. ORCID logoORCID: https://orcid.org/0000-0002-2895-9438, Namiki, S. ORCID logoORCID: https://orcid.org/0000-0003-1559-799X, Rubin, G.M. ORCID logoORCID: https://orcid.org/0000-0001-8762-8703, Sterne, G.R. ORCID logoORCID: https://orcid.org/0000-0002-7221-648X, Wolff, T. ORCID logoORCID: https://orcid.org/0000-0002-8681-1749 and Malkesman, O. ORCID logoORCID: https://orcid.org/0000-0003-2219-7476
eLife 12 : e80660. 23 February 2023

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. ORCID logoORCID: https://orcid.org/0000-0002-9830-2415, 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

This list was generated on Sun Jul 12 12:47:54 2026 UTC.
Open Access
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