Publications

Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de Mariscal, Constantin Pape, Tom Burke, Carlos Garcia-López-de Haro, Craig Russell, Luc\'ıa Moya-Sans, Cristina de-la Torre-Gutiérrez, Deborah Schmidt, Dominik Kutra, Maksim Novikov, Martin Weigert, Uwe Schmidt, Peter Bankhead, Guillaume Jacquemet, Daniel Sage, Ricardo Henriques, Arrate Muñoz-Barrutia, Emma Lundberg, Florian Jug, and Anna Kreshuk. BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis. bioRxiv, Cold Spring Harbor Laboratory, 2022. [PUMA: imported] URL

Liyuan Sui, Silvanus Alt, Martin Weigert, Natalie Dye, Suzanne Eaton, Florian Jug, Eugene W. Myers, Frank Jülicher, Guillaume Salbreux, and Christian Dahmann. Differential lateral and basal tension drive folding of Drosophila wing discs through two distinct mechanisms. Nature Communications, (9)1:4620, 2018. [PUMA: imported] URL

Falk Zakrzewski, Walter de Back, Martin Weigert, Torsten Wenke, Silke Zeugner, Robert Mantey, Christian Sperling, Katrin Friedrich, Ingo Roeder, Daniela Aust, Gustavo Baretton, and Pia Hönscheid. Automated detection of the HER2 gene amplification status in Fluorescence in situ hybridization images for the diagnostics of cancer tissues. Scientific Reports, (9)1:8231, 2019. [PUMA: imported]

Nicola Dietler, Matthias Minder, Vojislav Gligorovski, Augoustina Maria Economou, Denis Alain Henri Lucien Joly, Ahmad Sadeghi, Chun Hei Michael Chan, Mateusz Koziński, Martin Weigert, Anne-Florence Bitbol, and Sahand Jamal Rahi. A convolutional neural network segments yeast microscopy images with high accuracy. Nature Communications, (11)1:5723, 2020. [PUMA: imported] URL

Loic A Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F Sbalzarini, and Eugene W Myers. ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nature Methods, (12)6:480, Nature Publishing Group, 2015. [PUMA: imported]

Benjamin Gallusser, Max Stieber, and Martin Weigert. Self-supervised dense representation learning for live-cell microscopy with time arrow prediction. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2023. [PUMA: imported]

Yuhan Wang, Mark Eddison, Greg Fleishman, Martin Weigert, Shengjin Xu, Tim Wang, Konrad Rokicki, Cristian Goina, Fredrick E Henry, Andrew L Lemire, and others. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell, (184)26:6361--6377, Elsevier, 2021. [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. Medical image analysis, (92):103047, Elsevier, 2024. [PUMA: imported]

Mauro Gwerder, Cansaran Saygili Demir, Hannah L Williams, Alessandro Lugli, Cristina Graham Martinez, Joanna Kowal, Amjad Khan, Philipp Kirchner, Thibaud Koessler, Martin D Berger, and others. Morpho-molecular features of Epithelial Mesenchymal Transition associate with clinical outcome in patients with rectal cancer. bioRxiv, 2024--11, Cold Spring Harbor Laboratory, 2024. [PUMA: imported]

Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, and Eugene W. Myers. Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy. Nature Methods, (15)12:1090--1097, 2018. [PUMA: imported] URL

Evangelia Skoufa, Jixing Zhong, Oliver Kahre, Kelly Hu, Georgios Tsissios, Louise Carrau, Antonio Herrera, Albert Dominguez Mantes, Alejandro Castilla-Ibeas, Hwanseok Jang, Martin Weigert, Gioele La Manno, Matthias Lutolf, Marian Ros, and Can Aztekin. Specialized signaling centers direct cell fate and spatial organization in a limb organoid model. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: imported] URL

Michael Eisenstein. Smart solutions for automated imaging. Nature Methods, (17)11:1075--1079, Nature Publishing Group, 2020. [PUMA: imported]

Léo Bürgy, Martin Weigert, Georgios Hatzopoulos, Matthias Minder, Adrien Journé, Sahand Jamal Rahi, and Pierre Gönczy. CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets. BMC bioinformatics, (24)1:1--10, BioMed Central, 2023. [PUMA: imported]

Albert Dominguez Mantes, Antonio Herrera, Irina Khven, Anjalie Schlaeppi, Eftychia Kyriacou, Georgios Tsissios, Can Aztekin, Joachim Ligner, Gioele La Manno, and Martin Weigert. Spotiflow: accurate and efficient spot detection for imaging-based spatial transcriptomics with stereographic flow regression. bioRxiv, 2024--02, Cold Spring Harbor Laboratory, 2024. [PUMA: imported]

Robert Haase, Loic A Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, and Eugene W. Myers. CLIJ: GPU-accelerated image processing for everyone. Nature Methods, (17)1:5--6, Nature Publishing Group, 2020. [PUMA: imported]

Michael Eisenstein. AI under the microscope: the algorithms powering the search for cells.. Nature, (623)7989:1095--1097, 2023. [PUMA: imported]