Publications

Ni Li, Shorouq Zahra, Mariana Brito, Clare Flynn, Olof Görnerup, Koffi Worou, Murathan Kurfali, Chanjuan Meng, Wim Thiery, Jakob Zscheischler, Gabriele Messori, and Joakim Nivre. Using LLMs to Build a Database of Climate Extreme Impacts. Proceedings of the 1st Workshop on Natural Language Processing Meets Climate Change (ClimateNLP 2024), 93–110, Association for Computational Linguistics, 2024. [PUMA: imported zno] URL

Benjamin Gallusser, and Martin Weigert. Trackastra: Transformer-based cell tracking for live-cell microscopy. European Conference on Computer Vision, 467--484, 2025. [PUMA: ML_Spatial_Understanding imported]

Benjamin Gallusser, and Martin Weigert. Trackastra: Transformer-based cell tracking for live-cell microscopy. European Conference on Computer Vision, 467--484, 2025. [PUMA: imported]

Coleman Broaddus, Alexander Krull, Martin Weigert, Uwe Schmidt, and Gene Myers. Removing Structured Noise with Self-Supervised Blind-Spot Networks. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 159--163, 2020. [PUMA: imported]

Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, and Gene Myers. Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. WACV, 2020. [PUMA: imported]

Dora Mahecic, Willi L. Stepp, Chen Zhang, Juliette Griffié, Martin Weigert, and Suliana Manley. Event-driven acquisition for content-enriched microscopy. (19)10:1262--1267, 2022. [PUMA: imported] URL

Nils Wagner, Fynn Beuttenmueller, Nils Norlin, Jakob Gierten, Juan Carlos Boffi, Joachim Wittbrodt, Martin Weigert, Lars Hufnagel, Robert Prevedel, and Anna Kreshuk. Deep learning-enhanced light-field imaging with continuous validation. Nature Methods, (18)5:557--563, Nature Publishing Group, 2021. [PUMA: imported]

Andreas Müller, Deborah Schmidt, C Shan Xu, Song Pang, Joyson Verner D’Costa, Susanne Kretschmar, Carla Münster, Thomas Kurth, Florian Jug, Martin Weigert, Harald F Hess, and Solimena* Michele. 3D FIB-SEM reconstruction of microtubule--organelle interaction in whole primary mouse $\beta$ cells. JCB, The Rockefeller University Press, 2021. [PUMA: imported]

Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia-Ulloa, Eugene W Myers, Marius Ader, Irina Solovei, and Moritz Kreysing. Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice. eLife, (8):e49542, eLife Sciences Publications Limited, 2019. [PUMA: imported]

Andreas Müller, Deborah Schmidt, Lucas Rieckert, Michele Solimena, and Martin Weigert. Organelle-specific segmentation, spatial analysis, and visualization of volume electron microscopy datasets. arXiv preprint arXiv:2303.03876, 2023. [PUMA: imported]

Nina Vogt. Simulating the imaging process in scattering tissue. Nature methods, (15)6:406--406, Nature Publishing Group, 2018. [PUMA: imported]

Sarah Schmell, Falk Zakrzewski, Walter de Back, Martin Weigert, Uwe Schmidt, Torsten Wenke, Silke Zeugner, Robert Mantey, Christian Sperling, Ingo Roeder, Pia Hoenscheid, Daniela Aust, and Gustavo Baretton. An interpretable automated detection system for FISH-based HER2 oncogene amplification testing in histo-pathological routine images of breast and gastric cancer diagnostics. Medical Imaging with Deep Learning (MIDL), 2020. [PUMA: imported]

Andreas Müller, Deborah Schmidt, Jan Philipp Albrecht, Lucas Rieckert, Maximilian Otto, Leticia Elizabeth Galicia Garcia, Gunar Fabig, Michele Solimena, and Martin Weigert. Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nature Protocols, 1--31, Nature Publishing Group UK London, 2024. [PUMA: imported]

Martin Weigert, Loic Royer, Florian Jug, and Gene Myers. Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2017. [PUMA: imported]

Avinash Patel, Hyun Ou Lee, Louise M. Jawerth, S. K. Maharana, Marcus Jähnel, Marco Y Hein, Stoyno Stefanov Stoynov, Julia Mahamid, Shambaditya Saha, Titus M Franzmann, Andrej Pozniakovski, Ina Poser, Nicola Maghelli, Loic A. Royer, Martin Weigert, Eugene W. Myers, Stephan W Grill, David N. Drechsel, Anthony A. Hyman, and Simon Alberti. A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell, (162):1066-1077, 2015. [PUMA: imported]

Martin Weigert, and Uwe Schmidt. Nuclei Instance Segmentation and Classification in Histopathology Images with Stardist. 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 1-4, 2022. [PUMA: imported]

Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, and others. CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting. arXiv preprint arXiv:2303.06274, 2023. [PUMA: imported]

Rita Strack. Deep learning in imaging. Nature methods, (16)1:17--17, Nature Publishing Group, 2019. [PUMA: imported]

Mauricio Rocha-Martins, Elisa Nerli, Jenny Kretzschmar, Martin Weigert, Jaroslav Icha, Eugene W Myers, and Caren Norden. Neuronal migration prevents spatial competition in retinal morphogenesis. Nature, 1--10, Nature Publishing Group UK London, 2023. [PUMA: imported]

Quentin Juppet, Fabio De Martino, Elodie Marcandalli, Martin Weigert, Olivier Burri, Michael Unser, Cathrin Brisken, and Daniel Sage. Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features. Journal of Mammary Gland Biology and Neoplasia, Springer, 2021. [PUMA: imported]