Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes.
We present an application of nonlinear image registration to align in microscopy time lapse sequences for every frame the cell outline and interior with the outline and interior of the same cell in a reference frame. The registration relies on a subcellular fiducial marker, a cell motion mask, and a...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-12-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009667 |
| _version_ | 1811154341149540352 |
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| author | Xuexia Jiang Tadamoto Isogai Joseph Chi Gaudenz Danuser |
| author_facet | Xuexia Jiang Tadamoto Isogai Joseph Chi Gaudenz Danuser |
| author_sort | Xuexia Jiang |
| collection | DOAJ |
| description | We present an application of nonlinear image registration to align in microscopy time lapse sequences for every frame the cell outline and interior with the outline and interior of the same cell in a reference frame. The registration relies on a subcellular fiducial marker, a cell motion mask, and a topological regularization that enforces diffeomorphism on the registration without significant loss of granularity. This allows spatiotemporal analysis of extremely noisy and diffuse molecular processes across the entire cell. We validate the registration method for different fiducial markers by measuring the intensity differences between predicted and original time lapse sequences of Actin cytoskeleton images and by uncovering zones of spatially organized GEF- and GTPase signaling dynamics visualized by FRET-based activity biosensors in MDA-MB-231 cells. We then demonstrate applications of the registration method in conjunction with stochastic time-series analysis. We describe distinct zones of locally coherent dynamics of the cytoplasmic protein Profilin in U2OS cells. Further analysis of the Profilin dynamics revealed strong relationships with Actin cytoskeleton reorganization during cell symmetry-breaking and polarization. This study thus provides a framework for extracting information to explore functional interactions between cell morphodynamics, protein distributions, and signaling in cells undergoing continuous shape changes. Matlab code implementing the proposed registration method is available at https://github.com/DanuserLab/Mask-Regularized-Diffeomorphic-Cell-Registration. |
| first_indexed | 2024-04-10T04:14:01Z |
| format | Article |
| id | doaj.art-a578a16d6b3b4f64be128b8842cb3e76 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-10T04:14:01Z |
| publishDate | 2022-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-a578a16d6b3b4f64be128b8842cb3e762023-03-12T05:31:35ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-12-011812e100966710.1371/journal.pcbi.1009667Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes.Xuexia JiangTadamoto IsogaiJoseph ChiGaudenz DanuserWe present an application of nonlinear image registration to align in microscopy time lapse sequences for every frame the cell outline and interior with the outline and interior of the same cell in a reference frame. The registration relies on a subcellular fiducial marker, a cell motion mask, and a topological regularization that enforces diffeomorphism on the registration without significant loss of granularity. This allows spatiotemporal analysis of extremely noisy and diffuse molecular processes across the entire cell. We validate the registration method for different fiducial markers by measuring the intensity differences between predicted and original time lapse sequences of Actin cytoskeleton images and by uncovering zones of spatially organized GEF- and GTPase signaling dynamics visualized by FRET-based activity biosensors in MDA-MB-231 cells. We then demonstrate applications of the registration method in conjunction with stochastic time-series analysis. We describe distinct zones of locally coherent dynamics of the cytoplasmic protein Profilin in U2OS cells. Further analysis of the Profilin dynamics revealed strong relationships with Actin cytoskeleton reorganization during cell symmetry-breaking and polarization. This study thus provides a framework for extracting information to explore functional interactions between cell morphodynamics, protein distributions, and signaling in cells undergoing continuous shape changes. Matlab code implementing the proposed registration method is available at https://github.com/DanuserLab/Mask-Regularized-Diffeomorphic-Cell-Registration.https://doi.org/10.1371/journal.pcbi.1009667 |
| spellingShingle | Xuexia Jiang Tadamoto Isogai Joseph Chi Gaudenz Danuser Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. PLoS Computational Biology |
| title | Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. |
| title_full | Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. |
| title_fullStr | Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. |
| title_full_unstemmed | Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. |
| title_short | Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. |
| title_sort | fine grained nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes |
| url | https://doi.org/10.1371/journal.pcbi.1009667 |
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