Plant Phenotyping with Low Cost Digital Cameras and Image Analytics
In this paper we discuss a prototype, easy-to-deploy, and low cost (∼ $250) phenotype collection system for growth chambers. Off the shelf digital cameras, wireless transmitters, and PCs are used to store and process the images. A Matlab pipeline is used to fuse multiple images, identify the location of each Arabidopsis plant, segment its leaves, and measure leaf topology and area. Our early findings (unpublished) using this system for correlating genotype to phenotype are very promising. We hope that with future improvements and broad adoption, it will have the same disruptive effects as the first “build your own” microarrayers, which allowed for the explosion of genotyping information. Low cost genotyping and phenotyping will hopefully address some of the environmental, agricultural, and industrial sustainability challenges we are facing today.
KeywordsImage Fusion Complex Biological System Soil Water Deficit Phenotyping System Image Processing Module
Unable to display preview. Download preview PDF.
We would like to thank Prof. Borevitz (Department of Ecology and Evolution at University of Chicago) for providing us with the images and initial funding for this effort. Finally, we should thank Ron Hause, a graduate student from the Committee on Genetics, Genomics, and Systems Biology who did his rotation in Prof. Borevitz’s Lab, for his assistance in the development of this project.
- Pierre Crosson (1997). Impacts of Climate Change on Agriculture. Climate Issues Brief 4.Google Scholar
- Pittock, B. (2003).Climate change: An Australian Guide to the Science and Potential Impacts, Australian Greenhouse Office.Google Scholar
- William E. McClain (1997). Prairie establishment and landscaping. Nature Heritage Technical Publication.Google Scholar
- Tim Anderson (2009). How to Make Your Own Waterproof Camera Enclosure. Online [http://web.media.mit.edu/~tim/pix/waterproofcamera.html]
- Ronald J. Hause (2008). Deleting images with interval shooting. Online. [http://chdk.setepontos.com/index.php/topic,2003.0.html]
- Burt, P. J. and Kolczynski, R. J. (1993). Enhanced image capture through fusion. Computer Vision, 1993. Proceedings., Fourth International Conference on. pp 173-182.Google Scholar
- Wikipedia contributors (2008) YIQ. Wikipedia, The Free Encyclopedia. Online http://en.wikipedia.org/w/index.php?title=YIQ&oldid=259429685
- Li, C., Xu, C., Gui, C., and Fox, M. D. (2005). Level set evolution without re-initialization: a new variational formulation. CVPR 2005. IEEE Computer Society Conference on. 1: 430 – 436.Google Scholar
- DeRisi, J., Iyer, V, and Brown, P.O. (1998), The MGuide: A Complete Guide to Building Your Own Microarrayer. Stanford, CA, Stanford University 1998.Google Scholar