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Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution


Quantitative information on growing organs is required to better understand morphogenesis in both plants and animals. However, detailed analyses of growth patterns at cellular resolution have remained elusive. We developed an approach, multiangle image acquisition, three-dimensional reconstruction and cell segmentation–automated lineage tracking (MARS-ALT), in which we imaged whole organs from multiple angles, computationally merged and segmented these images to provide accurate cell identification in three dimensions and automatically tracked cell lineages through multiple rounds of cell division during development. Using these methods, we quantitatively analyzed Arabidopsis thaliana flower development at cell resolution, which revealed differential growth patterns of key regions during early stages of floral morphogenesis. Lastly, using rice roots, we demonstrated that this approach is both generic and scalable.

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Figure 1: MARS.
Figure 2: ALT.
Figure 3: Validation of MARS-ALT results.
Figure 4: Application of MARS-ALT to flower development.


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We thank A. Berger for help with establishing plant growth and imaging protocols; A. Lacroix for help with plant growth; and C. Lionnet for help with imaging. This work was funded by grants from the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (to J.-L.V.), the Region Languedoc-Roussillon (to R.F.) and from the Institut National de la Recherche en Informatique et en Automatique (to C.G.). P.D. was funded by a European Union Marie Curie Incoming International Fellowship grant (IIF-022002). The work of J.T. and C.G. was also funded by grants from the Agence Nationale de Recherche (Virtual Carpel, GeneShape and Flower model) and the European Union (Morphex).

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Authors and Affiliations



P.D., J.T., J.-L.V., G.M. and C.G. conceived the experiments; P.D. carried out the Arabidopsis experiments; J.-L.V. carried out the rice experiments; R.F., G.M. and C.G. conceived the software pipeline; R.F. wrote the software; R.F., E.M. and V.M. carried out the software experiments; E.M. and R.F. wrote the MARS-ALT documentation; P.D. and V.M. analyzed the output; P.D., G.M. and C.G. wrote the paper with input from the other authors.

Corresponding author

Correspondence to Christophe Godin.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9, Supplementary Table 1 and Supplementary Notes 1–7 (PDF 2916 kb)

Supplementary Video 1

Four-dimensional development of a flower from stage 0 to stage 3. The video shows the flower-A time course tracked over 70 h. Cells colored in red are those that are going to divide before the next time point. (MPG 4764 kb)

Supplementary Video 2

Backward tracing of sepal cells from early stage 3 to stage 0 (MPG 4354 kb)

Supplementary Video 3

Cut-away rendering of a rice root meristem (MPG 2542 kb)

Supplementary Software

MARS-ALT pipeline and documentation (ZIP 168685 kb)

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Fernandez, R., Das, P., Mirabet, V. et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat Methods 7, 547–553 (2010).

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