The iRoCS Toolbox - 3D analysis of the plant root apical meristem at cellular resolution

Plant Journal

Volumn 77, Issue 5, 2014, Pages 806-814

  Schmidt, Thorsten ^a   Pasternak, Taras ^a   Liu, Kun ^a   Blein, Thomas ^a,b   Aubry Hivet, Dorothée ^a   Dovzhenko, Alexander ^a   Duerr, Jasmin ^a   Teale, William ^a   Ditengou, Franck A ^a   Burkhardt, Hans ^a   Ronneberger, Olaf ^a   Palme, Klaus ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b INSTITUT JEAN PIERRE BOURGIN   (France)

Author keywords

Arabidopsis thaliana; automated image analysis; confocal microscopy; pin mutants; population studies; root modelling; technical advance

Indexed keywords

ARABIDOPSIS THALIANA; AUTOMATED IMAGE ANALYSIS; PIN MUTANTS; POPULATION STUDIES; ROOT MODELLING; TECHNICAL ADVANCES;

CELL PROLIFERATION; CONFOCAL MICROSCOPY; THREE DIMENSIONAL;

PLANTS (BOTANY);

ARABIDOPSIS THALIANA;

ARABIDOPSIS; CYTOLOGY; MERISTEM; MITOSIS; PLANT ROOT; THREE DIMENSIONAL IMAGING;

ARABIDOPSIS; IMAGING, THREE-DIMENSIONAL; MERISTEM; MITOSIS; PLANT ROOTS;

EID: 84896728784     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12429     Document Type: Article

References (31)

1. Aida, M., Beis, D., Heidstra, R., Willemsen, V., Blilou, I., Galinha, C., Nussaume, L., Noh, Y. S., Amasino, R., and, Scheres, B., (2004) The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell, 119, 109-120.
2. Beemster, G.T.S., and, Baskin, T.I., (1998) Analysis of cell division and elongation underlying the developmental acceleration of root growth in Arabidopsis thaliana. Plant Physiol. 116, 1515-1526.
3. Blilou, I., Xu, J., Wildwater, M., Willemsen, V., Paponov, I., Friml, J., Heidstra, R., Aida, M., Palme, K., and, Scheres, B., (2005) The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature, 433, 39-44.
4. Cui, H., Levesque, M.P., Vernoux, T., Jung, J.W., Paquette, A.J., Gallagher, K.L., Wang, J.Y., Blilou, I., Scheres, B., and, Benfey, P.N., (2007) An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science, 316, 421-425.
5. Dorr, A.E., Lerch, J., Spring, S., Kabania, N., and, Henkelman, R.M., (2008) High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57BL/6J mice. Neuroimage, 42, 60-69.
6. Emmenlauer, M., Ronneberger, O., Ponti, A., Schwarb, P., Griffa, A., Filippi, A., Nitschke, R., Driever, W., and, Burkhardt, H., (2009) XuvTools: free, fast and reliable stitching of large 3D datasets. J. Microsc. 233, 42-60.
7. Federici, F., Dupuy, L., Laplaze, L., Heisler, M., and, Haseloff, J., (2012) Integrated genetic and computation methods for in planta cytometry. Nat. Methods, 9, 483-485.
8. Fowlkes, C.C., Hendriks, C.L.L., Keränen, S.V., et al. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell, 133, 364-374.
9. Friml, J., Benkov, E., Blilou, I., et al. (2002) AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis. Cell, 108, 661-673.
10. Fujie, M., Kuroiwa, H., Kawano, S., and, Tsuneyoshi, K., (1993) Studies on the behavior of organelles and their nucleoids in the root apical meristem of Arabidopsis thaliana (L.) Col. Planta, 189, 443-452.
11. Helariutta, Y., Fukaki, H., Wysocka-Diller, J., Nakajima, K., Jung, J., Sena, G., and, Benfey, P.N., (2000) The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell, 101, 555-567.
12. Lein, E.S., Hawrylycz, M.J., Ao, N., et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445, 168-176.
13. Long, F., Peng, H., Liu, X., Kim, S.K., and, Myers, E., (2009) A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat. Methods, 6, 667-672.
14. Lowe, D.G., (2004) Distinctive image features from scale-invariant keypoints. Int. J. Comp. Vision, 60, 91-110.
15. Luengo Hendriks, C.L., Keränen, S.V., Fowlkes, C.C., et al. (2006) Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution. I: data acquisition pipeline. Genome Biol. 7, R123.
16. Malamy, J.E., and, Benfey, P.N., (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development, 124, 33-44.
17. Müller, A., Guan, C., Gälweiler, L., Tänzler, P., Huijser, P., Marchant, A., Parry, G., Bennett, M., Wisman, E., and, Palme, K., (1998) AtPIN2 defines a locus of Arabidopsis for root gravitropism control. EMBO J. 17, 6903-6911.
18. Ottenschläger, I., Wolff, P., Wolverton, C., Bhalerao, R.P., Sandberg, G., Ishikawa, H., Evans, M., and, Palme, K., (2003) Gravity-regulated differential auxin transport from columella to lateral root cap cells. Proc. Natl Acad. Sci. USA, 100, 2987-2991.
19. Paponov, I.A., Teale, W.D., Trebar, M., Blilou, I., and, Palme, K., (2005) The PIN auxin efflux facilitators: evolutionary and functional perspectives. Trends Plant Sci. 10, 170-177.
20. Petrášek, J., Mravec, J., Bouchard, R., et al. (2006) PIN proteins perform a rate-limiting function in cellular auxin efflux. Science, 312, 914-918.
21. Ronneberger, O., Liu, K., Rath, M., et al. (2012) ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat. Methods, 9, 735-742.
22. Santuari, L., Scacchi, E., Rodriguez-Villalon, A., Salinas, P., Dohmann, E.M., Brunoud, G., Vernoux, T., Smith, R.S., and, Hardtke, C.S., (2011) Positional information by differential endocytosis splits auxin response to drive Arabidopsis root meristem growth. Curr. Biol. 21, 1918-1923.
23. Schmidt, T., Keuper, M., Pasternak, T., Palme, K., and, Ronneberger, O., (2012) Modeling of sparsely sampled tubular surfaces using coupled curves. Lect. Notes Comput. Sci. 7476, 83-92.
24. Schulz, J., Schmidt, T., Ronneberger, O., Burkhardt, H., Pasternak, T., Dovzhenko, A., and, Palme, K., (2006) Fast scalar and vectorial grayscale based invariant features for 3D cell nuclei localization and classification. Lect. Notes Comput. Sci. 4174, 182-191.
25. Sena, G., Frentz, Z., Birnbaum, K.D., and, Leibler, S., (2011) Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. PLoS ONE, 6, e21303.
26. Shaw, S.L., and, Ehrhardt, D.W., (2013) Smaller, faster, brighter: advances in optical imaging of living plant cells. Annu. Rev. Plant Biol. 64, 351-375.
27. Skibbe, H., Reisert, M., Schmidt, T., Brox, T., Ronneberger, O., and, Burkhardt, H., (2012) Fast rotation invariant 3D feature computation utilizing efficient local neighborhood operators. IEEE Trans. Pattern Anal. Mach. Intell. 34, 1563-1575.
28. Truernit, E., Bauby, H., Dubreucq, B., Grandjean, O., Runions, J., Barthélémy, J., and, Palauqui, J.-C., (2008) High-resolution whole-mount imaging of three-dimensional tissue organization and gene expression enables the study of phloem development and structure in Arabidopsis. Plant Cell, 20, 1494-1503.
29. Ubeda-Tomás, S., Federici, F., Casimiro, I., Beemster, G.T., Bhalerao, R., Swarup, R., Doerner, P., Haseloff, J., and, Bennett, M.J., (2009) Gibberellin signaling in the endodermis controls arabidopsis root meristem size. Curr. Biol. 19, 1194-1199.
30. Vapnik, V.N., (1998) Statistical Learning Theory. Oxford, UK: Wiley Interscience.
31. Wuyts, N., Palauqui, J.-J., Conejero, G., Verdeil, J.-L., Granier, C., and, Massonnet, C., (2010) High-contrast three-dimensional imaging of the Arabidopsis leaf enables the analysis of cell dimensions in the epidermis and mesophyll. Plant Methods, 6, 17.