cefiler: cells files identifier
Within the context of analyzing the development of a conifer tree, the production and the differentiation of wood cells stemming from radial or spindled-shaped initial cells are relevant in the plant growth context, either from an endogenous (fluxes regulation or liber/wood exchanges) or exogenous (water resources or light conditions) point of view. Cell identification and counting are valuable methods to show the regularities of cell types (cambial growth for the initial cells, differentiation for the produced cells). Applying statistical methods on a sufficient number of samples is crucial for such an issue.
What is Cefiler ?
Cefiler is a fully-automated plugin devoted to the identification of cell files provided by light microscopic images. This module allows cellular type (vessel, fiber, parenchyma,…) to be defined and the geometry of each cell (wall or/and lumen area, wall thickness, circularity,…) to be characterized. The numerical results are saved in csv or xml files readable onto Clinex®.
Cefiler will not provide successful results in the following cases:
- on winter wood, where the lumen is smaller and darker ; when the color properties are reversed, the cell detection is very bad, as shown on the opposite side.
- on not enough contrasted images, by example the non colored images.
- The winter wood processing
- The non colored images processing
- actually unavailable as simple ImageJ plug-in : use the C-Toaster plug-in
- user guide
- Data (Pinus Negria)
- Data (Picnanthus)
- Data – blur study – (Pinus Negria)
- Data – lightness study – (Pinus Negria)
- Brunel, G. ; Borianne, P. ; Subsol, G. ; Jaeger, M. ; Caraglio, Y., 2014, Automatic Identification and Characterization of Radial Files in Light Microscopy Images of Wood. In : Annals of Botany, 114: 829-840, doi: 10.1093/aob/mcu119.
- Brunel, G.; Borianne, P.; Subsol, G.; G.; Jaeger, M., Caraglio, Y., 2013, Defining reliability coefficients in an automated method of identification and characterization of radial files in microscopic images of gymnosperms In Nygren, P., Lintunen, A., Godin, C., Nikinmaa, E., Sievänen, R. Eds, Proceedings of the 7th International Conference on Functional Structural Plant Models, Saariselka, Finland, 9 14 June 2013, pp. 82-84
- Brunel, G.; Borianne, P.; Subsol, G.; Jaeger, M., 2013, Simple-graphs fusion in image mosaic. Application to automated cell files identification in wood slices In Kämäräinen, J. K., Koskela, M. Eds, Image analysis : 18th Scandinavian Conference, SCIA 2013, Espoo, Finland, June 17-20, 2013. Proceedings, 2013, pp. 34-43
- Brunel, G.; Borianne, P.; Subsol, G.; Jaeger, M.; Caraglio, Y., 2012 Automatic charaterization of the cell organization in light microscopic images of wood: application to the identification of the cell fire In Guo, Y., Kang, M. Z., Dumont, Y. Eds, Plant growth modeling, simulation, visualization and applications. Proceedings PMA12 : The Fourth International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Shanghai, China, 31 October-3 November 2012, pp. 58-65
- Kennel, P.; Subsol, G.; Guéroult, M.; Borianne, P., 2010, Automatic identification of cell files in light microscopic images of conifer wood In Djemal, K., Deriche, M. Eds, 2010 2nd International conference on image processing theory, tools and applications, IPTA 2010, Paris, France, July 7-10, 2010, pp. 93-108
Bio: Y. Caraglio, C. Heinz, O. Taugourdeau, M. Guéroult
Dev: G. Brunel, P. Kennel, P. Borianne