Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells
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Abstract
High-throughput dynamic imaging of cells and organelles is essential for understanding complex cellular responses. We report Mantis, a high-throughput 4D microscope that integrates two complementary, gentle, live-cell imaging technologies: remote-refocus label-free microscopy and oblique light-sheet fluorescence microscopy. Additionally, we report shrimPy (Smart High-throughput Robust Imaging and Measurement in Python), an open-source software for high-throughput imaging, deconvolution, and single-cell phenotyping of 4D data. Using Mantis and shrimPy, we achieved high-content correlative imaging of molecular dynamics and the physical architecture of 20 cell lines every 15 min over 7.5 h. This platform also facilitated detailed measurements of the impacts of viral infection on the architecture of host cells and host proteins. The Mantis platform can enable high-throughput profiling of intracellular dynamics, long-term imaging and analysis of cellular responses to perturbations, and live-cell optical screens to dissect gene regulatory networks.
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Cites
Optical Pooled Screens in Human Cells
Feldman, D., Singh, A., Schmid-Burgk, J. L., Carlson, R. J., Mezger, A., Garrity, A. J., Zhang, F., & Blainey, P. C. (2019) · Cell · doi:10.1016/j.cell.2019.09.016 · Cited by 321 · see citing works
LIVECell—A large-scale dataset for label-free live cell segmentation
Edlund, C., Jackson, T. R., Khalid, N., Bevan, N., Dale, T., Dengel, A., Ahmed, S., Trygg, J., & Sjögren, R. (2021) · Nature Methods · doi:10.1038/s41592-021-01249-6 · Cited by 304 · see citing works
Integrated intracellular organization and its variations in human iPS cells
Viana, M. P., Chen, J., Knijnenburg, T. A., Vasan, R., Yan, C., Arakaki, J. E., Bailey, M., Berry, B., Borensztejn, A., Brown, E. M., et al. (2023) · Nature · doi:10.1038/s41586-022-05563-7 · Cited by 132 · see citing works
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- Authors
- Ivanov, I. E., Hirata-Miyasaki, E., Chandler, T., Cheloor-Kovilakam, R., Liu, Z., Pradeep, S., Liu, C., Bhave, M., Khadka, S., Arias, C., Leonetti, M. D., Huang, B., & Mehta, S. B.
- Affiliations
- Chan Zuckerberg Biohub San Francisco (US)
- University of California, San Francisco (US)
- Corresponding author
- Ivanov, Ivan E
- Huang, Bo
- Mehta, Shalin B
- ORCID
- Venue
- PNAS Nexus
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-08-09
- Volume
- 3
- Issue
- 9
- Pages
- pgae323-pgae323
- ISSN
- 2752-6542 (ISSN-L)
- PMC
- PMC11393572
- OpenAlex
- W4401449175
- Cited by
- 21
- References
- 3
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 6
- FWCI
- 4.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PNAS Nexus (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- Chan Zuckerberg Biohub
- National Institute of Health (R01GM131641)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Digital Holography and Microscopy
- Keywords
- deconvolution, single-cell phenotyping, correlative imaging, cellular architecture, intracellular dynamics, long-term live-cell imaging, gene regulatory networks
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