Hall, Hardy
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Abstract
While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to (1) segment radial plant organs into individual cells, (2) classify cells into cell type categories based upon Random Forest classification, (3) divide each cell into sub-regions, and (4) quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.
Keywords
automated image analysis; confocal microscopy; Arabidopsis; hypocotyl; automated phenotyping; code:matlab
Published in
Frontiers in Plant Science
2016, volume: 7, article number: 119
Publisher: FRONTIERS MEDIA SA
SLU Authors
Fakhrzadeh, Azadeh
- Uppsala University
Fischer, Urs
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
UKÄ Subject classification
Developmental Biology
Botany
Publication identifier
- DOI: https://doi.org/10.3389/fpls.2016.00119
Permanent link to this page (URI)
https://res.slu.se/id/publ/82702