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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Cell
2024
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/39532097/ |
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| _version_ | 1868266282443341826 |
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| author | Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi |
| author_facet | Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi |
| collection | PubMed - marine biology |
| contents | Spatiotemporal modeling of molecular holograms. Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi Animals Mice Holography Embryonic Development Spatio-Temporal Analysis Cell Movement Imaging, Three-Dimensional Embryo, Mammalian Organogenesis Heart Quantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo (https://github.com/aristoteleo/spateo-release), a 3D spatiotemporal modeling framework, and applied it to a 3D mouse embryogenesis atlas at E9.5 and E11.5, capturing eight million cells. Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to create molecular holograms of whole embryos. It introduces digitization methods to uncover multi-level biology from subcellular to whole organ, identifying expression gradients along orthogonal axes of emergent 3D structures, e.g., secondary organizers such as midbrain-hindbrain boundary (MHB). Spateo further jointly models intercellular and intracellular interaction to dissect signaling landscapes in 3D structures, including the zona limitans intrathalamica (ZLI). Lastly, Spateo introduces "morphometric vector fields" of cell migration and integrates spatial differential geometry to unveil molecular programs underlying asymmetrical murine heart organogenesis and others, bridging macroscopic changes with molecular dynamics. Thus, Spateo enables the study of organ ecology at a molecular level in 3D space over time. |
| format | Artículo científico |
| id | pubmed_39532097 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | Cell |
| record_format | pubmed |
| spellingShingle | Spatiotemporal modeling of molecular holograms. Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi Animals Mice Holography Embryonic Development Spatio-Temporal Analysis Cell Movement Imaging, Three-Dimensional Embryo, Mammalian Organogenesis Heart Spatiotemporal modeling of molecular holograms. Qiu, Xiaojie Zhu, Daniel Y Lu, Yifan Yao, Jiajun Jing, Zehua Min, Kyung Hoi Cheng, Mengnan Pan, Hailin Zuo, Lulu King, Samuel Fang, Qi Zheng, Huiwen Wang, Mingyue Wang, Shuai Zhang, Qingquan Yu, Sichao Liao, Sha Liu, Chao Wu, Xinchao Lai, Yiwei Hao, Shijie Zhang, Zhewei Wu, Liang Zhang, Yong Li, Mei Tu, Zhencheng Lin, Jinpei Yang, Zhuoxuan Li, Yuxiang Gu, Ying Ellison, David Chen, Ao Liu, Longqi Weissman, Jonathan S Ma, Jiayi Xu, Xun Liu, Shiping Bai, Yinqi Animals Mice Holography Embryonic Development Spatio-Temporal Analysis Cell Movement Imaging, Three-Dimensional Embryo, Mammalian Organogenesis Heart Quantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo (https://github.com/aristoteleo/spateo-release), a 3D spatiotemporal modeling framework, and applied it to a 3D mouse embryogenesis atlas at E9.5 and E11.5, capturing eight million cells. Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to create molecular holograms of whole embryos. It introduces digitization methods to uncover multi-level biology from subcellular to whole organ, identifying expression gradients along orthogonal axes of emergent 3D structures, e.g., secondary organizers such as midbrain-hindbrain boundary (MHB). Spateo further jointly models intercellular and intracellular interaction to dissect signaling landscapes in 3D structures, including the zona limitans intrathalamica (ZLI). Lastly, Spateo introduces "morphometric vector fields" of cell migration and integrates spatial differential geometry to unveil molecular programs underlying asymmetrical murine heart organogenesis and others, bridging macroscopic changes with molecular dynamics. Thus, Spateo enables the study of organ ecology at a molecular level in 3D space over time. |
| title | Spatiotemporal modeling of molecular holograms. |
| topic | Animals Mice Holography Embryonic Development Spatio-Temporal Analysis Cell Movement Imaging, Three-Dimensional Embryo, Mammalian Organogenesis Heart |
| url | https://pubmed.ncbi.nlm.nih.gov/39532097/ |