Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images

PLoS Computational Biology

Volumn 9, Issue 4, 2013, Pages

  Failmezger, Henrik ^a,b   Jaegle, Benjamin ^b   Schrader, Andrea ^b   Hülskamp, Martin ^b   Tresch, Achim ^a,b  

^a MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PLANTS (BOTANY); SPATIAL VARIABLES MEASUREMENT; THREE DIMENSIONAL COMPUTER GRAPHICS;

DOUBLE MUTANTS; GENE REGULATORY NETWORKS; INHIBITING FACTORS; LEAF SURFACES; MICROSCOPIC IMAGE; PATHOGEN RESISTANCE; PHENOTYPIC VARIATIONS; PROMOTING FACTORS; SINGLE CELLS; SINGLE MUTANT;

IMAGE RECONSTRUCTION;

ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DEVELOPMENTAL STAGE; IMAGE ANALYSIS; IMAGE RECONSTRUCTION; INTERMETHOD COMPARISON; LEAF DEVELOPMENT; MICROSCOPE IMAGE; NONHUMAN; PLANT LEAF; QUANTITATIVE ANALYSIS; THREE DIMENSIONAL IMAGING; TRICHOME;

EID: 84876912158     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003029     Document Type: Article

References (26)

1. Hulskamp M, Misra S, Jurgens G, (1994) Genetic dissection of trichome cell development in Arabidopsis. Cell 76: 555-566.
2. Andriankaja M, Dhondt S, De Bodt S, Vanhaeren H, Coppens F, et al. (2012) Exit from proliferation during leaf development in Arabidopsis thaliana: a not-so-gradual process. Developmental cell 22: 64-78.
3. Pesch M, Hulskamp M, (2009) One, two, three...models for trichome patterning in Arabidopsis? Curr Opin Plant Biol 12: 587-592.
4. Tominaga-Wada R, Ishida T, Wada T, (2011) New insights into the mechanism of development of Arabidopsis root hairs and trichomes. International review of cell and molecular biology 286: 67-106.
5. Balkunde R, Pesch M, Hulskamp M, (2010) Trichome patterning in Arabidopsis thaliana from genetic to molecular models. Current topics in developmental biology 91: 299-321.
6. Balkunde R, Bouyer D, Hulskamp M, (2011) Nuclear trapping by GL3 controls intercellular transport and redistribution of TTG1 protein in Arabidopsis. Development 138: 5039-5048.
7. Lee K, Avondo J, Morrison H, Blot L, Stark M, et al. (2006) Visualizing plant development and gene expression in three dimensions using optical projection tomography. Plant Cell 18: 2145-2156.
8. Kaminuma E, Yoshizumi T, Wada T, Matsui M, Toyoda T, (2008) Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X-ray computed tomography. Plant J 56: 470-482.
9. Greese B, Wester K, Bensch R, Ronneberger O, Timmer J, et al. (2012) Influence of cell-to-cell variability on spatial pattern formation. IET systems biology 6: 143-153.
10. Bensch R, Ronneberger O, Greese B, Fleck C, Wester K, et al. (2010) Image analysis of arabidopsis trichome patterning in 4D confocal datasets. In: International Symposium on Biomedical Imaging: From Nano to Macro; 28 June-1 July 2009 Boston, Massachusetts, United states. ISBI 2009. Available;http://lmb.informatik.uni-freiburg.de/Publications/2009/BRB09/.
11. Valdecasas AG, Marshall D, Becerra JM, Terrero J, (2001) On the extended depth of focus algorithms for bright field microscopy. Micron 32: 559-569.
12. Forster B, Van De Ville D, Berent J, Sage D, Unser M, (2004) Complex wavelets for extended depth-of-field: A new method for the fusion of multichannel microscopy images. Microscopy Research and technique 65: 33-42.
13. Aguet F, Van De Ville D, Unser M (2008) Model-Based 2.5-D Deconvolution for Extended Depth of Field in Brightfield Microscopy. In: IEEE Transactions on Image Processing. pp. 1144-1153.
14. Tessens L, Ledda A, Pizurica A, Philips W. (2007) Extending the depth of field in microscopy through curvelet-based frequency-adaptive image fusion. In: IEEE International Conference on Acoustics, Speech and Signal Processing; 15-20 April 2007. pp. I-861-I-864.
15. Piccinini F, Tesei A, Zoli W, Bevilacqua A, (2012) Extended depth of focus in optical microscopy: Assessment of existing methods and a new proposal. Microscopy Research and Technique 75: 1582-1592.
16. Kittler J, (1983) On the accuracy of the Sobel edge detector. Image and Vision Computing 1: 37-42.
17. Xavier-Vidal R, (2009) Disector Z-axis mechanical method for stereology. Annals of the Brazilian Academy of Sciences 82: 539-544.
18. Gorban A, Zinovyev A, (2005) Elastic principal graphs and manifolds and their practical applications. Computing 75: 359-379.
19. Szymanski DB, Jilk RA, Pollock SM, Marks MD, (1998) Control of GL2 expression in Arabidopsis leaves and trichomes. Development 125: 1161-1171.
20. Schellmann S, Schnittger A, Kirik V, Wada T, Okada K, et al. (2002) TRIPTYCHON and CAPRICE mediate lateral inhibition during trichome and root hair patterning in Arabidopsis. Embo J 21: 5036-5046.
21. Larkin LC, Oppenheimer DG, Lloyd AM, Paparozzi ET, Marks MD, (1994) The roles of the GLABROUS1 and TRANPARENT TESTA GLABRA genes in Arabidopsis trichome development. The Plant Cell 6: 1065-1076.
22. Kurata T, Ishida T, Kawabata-Awai C, Noguchi M, Hattori S, et al. (2005) Cell-to-cell movement of the CAPRICE protein in Arabidopsis root epidermal cell differentiation. Development 132: 5387-5398.
23. Otsu N, (1979) A Threshold Selection Method from Gray-Level Histograms. Systems, Man and Cybernetics, IEEE Transactions on 9: 62-66.
24. Soille P (2010) Morphological Image Analysis: Principles and Applications. Springer. 408 p.
25. Deschamps T, Cohen LD, (2001) Fast extraction of minimal paths in 3D images and applications to virtual endoscopy. Medical Image Analysis 5: 281-299.
26. Sethian JA (1999) Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science. Cambridge University Press. 378 p.