Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals
Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord.
Authors
- Erin M. Carey
- Michael E. Reitman (ORCID: https://orcid.org/0000-0001-9655-5390)
- Haohui Deng (ORCID: https://orcid.org/0000-0001-5948-9101)
- Daniela Duarte
- Xuelong Mi
- Weizhan Zhang (ORCID: https://orcid.org/0000-0003-0330-5435)
- C R Taylor (ORCID: https://orcid.org/0000-0002-4167-2546)
- Misha B. Ahrens (ORCID: https://orcid.org/0000-0002-3457-4462)
- Jing-Xuan Lim (ORCID: https://orcid.org/0000-0002-5983-9164)
- Song-Hai Shi
- Kira E. Poskanzer (ORCID: https://orcid.org/0000-0003-4830-8891)
- Guoqiang Yu (ORCID: https://orcid.org/0000-0002-6743-7413)
- David A. Lyons (ORCID: https://orcid.org/0000-0003-1166-4454)
- Alex Chen (ORCID: https://orcid.org/0000-0003-3950-4460)
- Rafael Almeida (ORCID: https://orcid.org/0000-0003-3563-5463)
- Xiaoyu Wang (ORCID: https://orcid.org/0000-0002-4696-5460)
- Axel Nimmerjahn (ORCID: https://orcid.org/0000-0002-0875-7855)
- Mark Bright
- Philipp N. Braaker
- Virginia M. S. Ruetten (ORCID: https://orcid.org/0000-0003-0073-2861)
- Lei Li (ORCID: https://orcid.org/0000-0001-6990-1825)
- Mengfan Wang (ORCID: https://orcid.org/0000-0003-3370-6395)
- Wei Zheng (ORCID: https://orcid.org/0000-0002-2984-9003)
- Yongkang Huang (ORCID: https://orcid.org/0000-0002-4811-001X)
- Yizhi Wang (ORCID: https://orcid.org/0000-0001-9456-0743)
Institutions
- Salk Institute for Biological Studies (US)
- Howard Hughes Medical Institute (US)
- Janelia Research Campus (US)
- Fudan University (CN)
- State Key Laboratory of Medical Neurobiology
- Virginia Tech (US)
- University of Edinburgh (GB)
- Tsinghua University (CN)
Publication Details
- Journal
- Cell
- Published
- 2025-04-08
- DOI
- https://doi.org/10.1016/j.cell.2025.03.012
- Citations
- 15
- Primary Topic
- Metabolomics and Mass Spectrometry Studies
- Type
- article
- Field-Weighted Citation Impact
- 12.09
Funders
- National Science Foundation
- National Institutes of Health