Publications

Matthew R King, Kiersten M Ruff, Andrew Z Lin, Avnika Pant, Mina Farag, Jared Lalmansingh, Tingting Wu, Wei Ouyang, Martin J Fossat, Matthew D Lew, others (2023). Macromolecular Condensation Organizes Nucleolar Sub-Phases to Set Up a pH Gradient. Available at SSRN 4520791.

Christophe Zimmer, Wei Ouyang (2023). Method, device, and computer program for improving the reconstruction of dense super-resolution images from diffraction-limited images acquired by single molecule localization microscopy.

Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E Diel, others (2023). OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv.

Wei Ouyang, Kevin W Eliceiri, Beth A Cimini (2023). Moving beyond the desktop: prospects for practical bioimage analysis via the web. Frontiers in Bioinformatics.

Carlos Garcia Lopez de Haro, Stephane Dallongeville, Thomas Musset, Estibaliz Gomez de Mariscal, Daniel Sage, Wei Ouyang, Arrate Munoz-Barrutia, Jean-Yves Tinevez, Jean-Christophe Olivo-Marin (2023). JDLL: A library to run Deep Learning models on Java bioimage informatics platforms. arXiv preprint arXiv:2306.04796.

Graham T Johnson, Eran Agmon, Matthew Akamatsu, Emma Lundberg, Blair Lyons, Wei Ouyang, Omar A Quintero-Carmona, Megan Riel-Mehan, Susanne Rafelski, Rick Horwitz (2023). Building the next generation of virtual cells to understand cellular biology. Biophysical Journal.

Wanlu Lei, Caterina Fuster-Barceló, Arrate Munoz-Barrutia, Wei Ouyang (2023). BioImage. IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base. arXiv preprint arXiv:2310.18351.

Matthew R King, Andrew Z Lin, Kiersten M Ruff, Mina Farag, Wei Ouyang, Michael D Vahey, Emma Lundberg, Rohit V Pappu (2022). Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers. bioRxiv.

Jayasankar Mohanakrishnan Kaimal, Marianna Tampere, Trang H Le, Ulrika Axelsson, Hao Xu, Hanna Axelsson, Anna Backstrom, Francesco Marabita, Elisabeth Moussaud-Lamodiere, Duncan Njenda, others (2022). Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing (preprint).

Wei Ouyang, Jiachuan Bai, Manish Kumar Singh, Christophe Leterrier, Paul Barthelemy, Samuel FH Barnett, Teresa Klein, Markus Sauer, Pakorn Kanchanawong, Nicolas Bourg, others (2022). ShareLoc—an open platform for sharing localization microscopy data. Nature Methods.

Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller (2022). FISH-quant v2: a scalable and modular tool for smFISH image analysis. Rna.

Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gomez de Mariscal, Constantin Pape, Tom Burke, Carlos Garcia Lopez de Haro, Craig Russell, Lucı́a Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, others (2022). Bioimage model zoo: a community-driven resource for accessible deep learning in bioimage analysis. bioRxiv.

Trang Le, Casper F Winsnes, Ulrika Axelsson, Hao Xu, Jayasankar Mohanakrishnan Kaimal, Diana Mahdessian, Shubin Dai, Ilya S Makarov, Vladislav Ostankovich, Yang Xu, others (2022). Analysis of the human protein atlas weakly supervised single-cell classification competition. Nature Methods.

Wei Ouyang, Richard W Bowman, Haoran Wang, Kaspar E Bumke, Joel T Collins, Ola Spjuth, Jordi Carreras-Puigvert, Benedict Diederich (2022). An Open-Source Modular Framework for Automated Pipetting and Imaging Applications. Advanced biology.

Xian Hao, Jyotsana J Parmar, Benoı̂t Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer (2021). Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures. Genome biology.

Henry Pinkard, Nico Stuurman, Ivan E Ivanov, Nicholas M Anthony, Wei Ouyang, Bin Li, Bin Yang, Mark A Tsuchida, Bryant Chhun, Grace Zhang, others (2021). Pycro-Manager: open-source software for customized and reproducible microscope control. Nature methods.

Wei Ouyang, Trang Le, Hao Xu, Emma Lundberg (2021). Interactive biomedical segmentation tool powered by deep learning and ImJoy. F1000Research.

Estibaliz Gomez de Mariscal, Carlos Garcı́a-López-de-Haro, Wei Ouyang, Laurene Donati, Emma Lundberg, Michael Unser, Arrate Munoz-Barrutia, Daniel Sage (2021). DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nature Methods.

Yue Qin, Edward L Huttlin, Casper F Winsnes, Maya L Gosztyla, Ludivine Wacheul, Marcus R Kelly, Steven M Blue, Fan Zheng, Michael Chen, Leah V Schaffer, others (2021). A multi-scale map of cell structure fusing protein images and interactions. Nature.

Christophe Zimmer, Wei Ouyang (2020). Method, device, and computer program for improving the reconstruction of dense super-resolution images from diffraction-limited images acquired by single molecule localization microscopy.

Lovisa Stenström, Diana Mahdessian, Christian Gnann, Anthony J Cesnik, Wei Ouyang, Manuel D Leonetti, Mathias Uhlén, Sara Cuylen-Haering, Peter J Thul, Emma Lundberg (2020). Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Molecular systems biology.

Wei Ouyang, Florian Mueller, Martin Hjelmare, Emma Lundberg, Christophe Zimmer (2019). ImJoy: an open-source computational platform for the deep learning era. Nature methods.

Wei Ouyang, Casper F Winsnes, Martin Hjelmare, Anthony J Cesnik, Lovisa Åkesson, Hao Xu, Devin P Sullivan, Shubin Dai, Jun Lan, Park Jinmo, others (2019). Analysis of the human protein atlas image classification competition. Nature methods.

Wei Ouyang, Andrey Aristov, Mickaël Lelek, Xian Hao, Christophe Zimmer (2018). Deep learning massively accelerates super-resolution localization microscopy. Nature biotechnology.

Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Wei Ouyang, Christophe Zimmer, Marion Peter, Edouard Bertrand, Thomas Walter, Florian Mueller (2018). A computational framework to study sub-cellular RNA localization. Nature Communications.

Wei Ouyang, Christophe Zimmer (2017). The imaging tsunami: computational opportunities and challenges. Current Opinion in Systems Biology.

Geng Yang, Mingzhe Jiang, Wei Ouyang, Guangchao Ji, Haibo Xie, Amir M Rahmani, Pasi Liljeberg, Hannu Tenhunen (2017). IoT-based remote pain monitoring system: From device to cloud platform. IEEE journal of biomedical and health informatics.