2026

A generative AI framework for disease-specific lung microtissue bioengineering.
Bahry, Ella ORCID: https://orcid.org/0000-0002-6358-2576, Pestoni, Jeanine C., Hirzel, Kai, Savchyn, Taras, Porras-Gonzalez, Diana, Getmanchuk-Zaporoshchenko, Vera, Gregor, Martin, Conlon, Thomas M, Önder Yildirim, Ali, Harrington, Kyle ORCID: https://orcid.org/0000-0002-7237-1973, Schmidt, Deborah ORCID: https://orcid.org/0000-0002-8621-9438, Burgstaller, Gerald and Heymann, Michael
bioRxiv : 2026.04.15.718723. 16 April 2026

2025

Image Dataset: A generative AI framework enables disease-specific tissue bioengineering.
Pestoni, Jeanine Chantal, Bahry, Ella ORCID: https://orcid.org/0000-0002-6358-2576, Hirzel, Kai, Heymann, Michael ORCID: https://orcid.org/0000-0002-9278-8207, Burgstaller, Gerald ORCID: https://orcid.org/0000-0002-7121-2567 and Schmidt, Deborah ORCID: https://orcid.org/0000-0002-8621-9438
[Dataset] 16 December 2025

A human missense variant in BSX decouples circadian behaviour from metabolic rhythmicity while preserving lifespan in mice.
Treier, Anna-Corina ORCID: https://orcid.org/0000-0003-1309-6446, Klasen, Christian, Kramer, Madlen, Schmidt, Deborah ORCID: https://orcid.org/0000-0002-8621-9438, Block, Franziska, Gebhardt, Janine, Rusak, Fabio Rojas ORCID: https://orcid.org/0000-0002-0637-9467, Farooqi, I. Sadaf ORCID: https://orcid.org/0000-0001-7609-3504 and Treier, Mathias ORCID: https://orcid.org/0000-0002-8751-1246
bioRxiv : 2025.12.05.692520. 9 December 2025

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

PD-L1 expression assessment in Angiosarcoma improves with artificial intelligence support.
Reith, F.H. ORCID: https://orcid.org/0000-0002-0745-2726, Jarosch, A., Albrecht, J.P. ORCID: 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: https://orcid.org/0000-0002-9830-2415
Journal of Pathology Informatics 18 : 100447. August 2025

Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification.
Giese, W. ORCID: https://orcid.org/0000-0003-0872-0929, Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695, Oppenheim, O. ORCID: https://orcid.org/0000-0002-5299-3193, Akmeriç, E.B. ORCID: https://orcid.org/0000-0003-4463-8017, Kraxner, J. ORCID: https://orcid.org/0000-0002-3515-7468, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384
Nature Communications 16 (1): 1474. 8 February 2025

2024

Structure, interaction and nervous connectivity of beta cell primary cilia.
Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Klena, N. ORCID: https://orcid.org/0000-0002-2631-2294, Pang, S. ORCID: https://orcid.org/0000-0002-7231-4151, Garcia, L.E.G., Topcheva, O. ORCID: https://orcid.org/0000-0003-2010-2410, Aurrecoechea Duran, S., Sulaymankhil, D., Seliskar, M., Mziaut, H., Schöniger, E., Friedland, D., Kipke, N., Kretschmar, S., Münster, C., Weitz, J., Distler, M., Kurth, T. ORCID: https://orcid.org/0000-0001-5624-1717, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Hess, H.F. ORCID: https://orcid.org/0000-0003-3000-1533, Xu, C.S. ORCID: https://orcid.org/0000-0002-8564-7836, Pigino, G. and Solimena, M. ORCID: https://orcid.org/0000-0002-3653-8107
Nature Communications 15 (1): 9168. 24 October 2024

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A. ORCID: https://orcid.org/0000-0003-1783-5533, Kim, S.J. ORCID: https://orcid.org/0000-0001-8357-0073, Thomas, G., Farsi, Z. ORCID: https://orcid.org/0000-0001-7274-981X, Zolotarov, G. ORCID: https://orcid.org/0000-0002-3971-3070, Dube, G., Deter, A., Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Georgii, E., Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
EMBO Reports 25 (7): 3039. July 2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695, Rieckert, L., Otto, M. ORCID: https://orcid.org/0009-0003-1919-5880, Galicia Garcia, L.E. ORCID: https://orcid.org/0009-0006-7891-7785, Fabig, G. ORCID: https://orcid.org/0000-0003-3017-0978, Solimena, M. and Weigert, M. ORCID: https://orcid.org/0000-0002-7780-9057
Nature Protocols 19 (5): 1436-1466. May 2024

2023

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L. ORCID: https://orcid.org/0000-0002-7225-7011, Franzen, J. ORCID: https://orcid.org/0000-0002-0761-641X, Hirsch, P. ORCID: https://orcid.org/0000-0002-2353-5310, Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695 and Kainmueller, D. ORCID: 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

VoltRon: a spatial omics analysis platform for multi-resolution and multi-omics integration using image registration.
Manukyan, A. ORCID: https://orcid.org/0000-0002-0441-9517, Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Becher, E., Pascual-Reguant, Anna, Plumbom, I. ORCID: https://orcid.org/0009-0006-3720-3700, Dikmen, H.O., Elezkurtaj, S., Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Hauser, A.E., Hocke, A., Radbruch, H. ORCID: https://orcid.org/0000-0001-6941-3397, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
bioRxiv : 2023.12.15.571667. 15 December 2023

2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Breimann, L. ORCID: https://orcid.org/0000-0001-7702-5749, Zouinkhi, M. ORCID: https://orcid.org/0000-0002-9441-2908, Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Lionnet, T. ORCID: https://orcid.org/0000-0003-1508-0202 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Nature Methods 19 (12): 1563-1567. December 2022

BioImage Model Zoo: a community-driven resource for accessible deep learning in bioimage analysis.
Ouyang, W., Beuttenmueller, F., Gómez-de-Mariscal, E., Pape, C., Burke, T., Garcia-López-de-Haro, C., Russell, C., Moya-Sans, L., de-la-Torre-Gutiérrez, C., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Kutra, D., Novikov, M., Weigert, M., Schmidt, U., Bankhead, P., Jacquemet, G., Sage, D., Henriques, R., Muñoz-Barrutia, A., Lundberg, E., Jug, F. and Kreshuk, A.
bioRxiv : 2022.06.07.495102. 8 June 2022

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R., Nagathihalli Kantharaju, M., Haruvi, R., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Kawashima, T.
Frontiers in Cell and Developmental Biology 10 : 875044. 19 May 2022

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Tomancak, P., Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P. ORCID: https://orcid.org/0000-0002-2353-5310, Epstein, L. and Guignard, L. ORCID: https://orcid.org/0000-0002-3686-1385
In: Cell Movement in Health and Disease. Academic Press, London, 341-361. ISBN 978-0-323-90195-6 2022

2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L., Dubois, Z., Smith, J., Lee, Y. ORCID: https://orcid.org/0000-0001-7478-2672 and Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973
Biosystems 208 : 104483. October 2021

3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.
Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Xu, C.S. ORCID: https://orcid.org/0000-0002-8564-7836, Pang, S. ORCID: https://orcid.org/0000-0002-7231-4151, D'Costa, J.V. ORCID: https://orcid.org/0000-0001-5985-907X, Kretschmar, S., Münster, C., Kurth, T. ORCID: https://orcid.org/0000-0001-5624-1717, Jug, F., Weigert, M., Hess, H.F. ORCID: https://orcid.org/0000-0003-3000-1533 and Solimena, M. ORCID: https://orcid.org/0000-0002-3653-8107
Journal of Cell Biology 220 (2): e202010039. 1 February 2021

DenoiSeg: joint denoising and segmentation.
Buchholz, T.O. ORCID: https://orcid.org/0000-0001-6953-8915, Prakash, M. ORCID: https://orcid.org/0000-0002-6351-0281, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Krull, A. ORCID: https://orcid.org/0000-0002-7778-7169 and Jug, F. ORCID: https://orcid.org/0000-0002-8499-5812
Lecture Notes in Computer Science 12535 : 324-337. 10 January 2021

2020

CLIJ: GPU-accelerated image processing for everyone.
Haase, R., Royer, L.A., Steinbach, P., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Dibrov, A., Schmidt, U., Weigert, M., Maghelli, N., Tomancak, P., Jug, F. and Myers, E.W.
Nature Methods 17 (1): 5-6. January 2020

2019

A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage.
Sharir, A., Marangoni, P., Zilionis, R., Wan, M., Wald, T., Hu, J.K., Kawaguchi, K., Castillo-Azofeifa, D., Epstein, L., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Pagella, P. ORCID: https://orcid.org/0000-0001-6912-0957, Mitsiadis, T., Siebel, C.W., Klein, A.M. ORCID: https://orcid.org/0000-0001-8913-7879 and Klein, O.D. ORCID: https://orcid.org/0000-0002-6254-7082
Nature Cell Biology 21 (9): 1102-1112. September 2019

2018

Content-aware image restoration: pushing the limits of fluorescence microscopy.
Weigert, M. ORCID: https://orcid.org/0000-0002-7780-9057, Schmidt, U., Boothe, T. ORCID: https://orcid.org/0000-0003-1925-0213, Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Dibrov, A., Jain, A. ORCID: https://orcid.org/0000-0003-4704-7992, Wilhelm, B. ORCID: https://orcid.org/0000-0003-1608-5267, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Broaddus, C., Culley, S. ORCID: https://orcid.org/0000-0003-2112-0143, Rocha-Martins, M., Segovia-Miranda, F., Norden, C. ORCID: https://orcid.org/0000-0001-8835-1451, Henriques, R., Zerial, M., Solimena, M., Rink, J., Tomancak, P. ORCID: https://orcid.org/0000-0002-2222-9370, Royer, L. ORCID: https://orcid.org/0000-0002-9991-9724, Jug, F. ORCID: https://orcid.org/0000-0002-8499-5812 and Myers, E.W.
Nature Methods 15 (12): 1090-1097. December 2018

2014

Bridging the Gap: Methods and Teaching of F-A-S-T - Framing-Art-Science-Technology.
Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Koalick, G., Gassel, S., Sery, C., Groh, R. and Wacker, M.
Lecture Notes in Computer Science 8517 : 589-600. 2014

2013

Developing mobile interface metaphors and gestures.
Kammer, D., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Keck, M. and Groh, R.
In: 15th International Conference on Human-Computer Interaction with Mobile Devices and Services, MobileHCI 2013, 27-30 August 2013, Munich, Germany. 27 August 2013