Automated Analysis of Human Protein Atlas Immunofluorescence Images. - Justin Newberg; Jieyue Li; Arvind Rao; Fredrik Ponten; Mathias Uhlen; Emma Lundberg; Robert F. Murphy (ISBI, 2009)

ImJoy: an open-source computational platform for the deep learning era. - Wei Ouyang 001; Florian Mueller; Martin Hjelmare; Emma Lundberg; Christophe Zimmer (CoRR, 2019)

Interactive biomedical segmentation tool powered by deep learning and ImJoy. - Wei Ouyang 001; Trang Le; Hao Xu; Emma Lundberg (F1000Research, 2021)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research. - James Burgess; Jeffrey J. Nirschl; Laura Bravo-Sánchez; Alejandro Lozano; Sanket Rajan Gupte; Jesus G. Galaz-Montoya; Yuhui Zhang; Yuchang Su; Disha Bhowmik; Zachary Coman; Sarina M. Hasan; Alexandra Johannesson; et al. (CVPR, 2025)

CellFlow: Simulating Cellular Morphology Changes via Flow Matching. - Yuhui Zhang; Yuchang Su; Chenyu Wang 003; Tianhong Li; Zoe Wefers; Jeffrey J. Nirschl; James Burgess; Daisy Ding; Alejandro Lozano; Emma Lundberg; Serena Yeung-Levy (CoRR, 2025)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)