"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.

Manuscript

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography", K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen

Sumplementary Material

Datasets used in Figures

Optical Projection Tomograpy dataset, for figures 1 and 2. [1]

Software

QtVolViewerLITE v1

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

QtVolViewerLITEv1.zip | QuickStart.pdf | UserManual.pdf

QtVolViewer v1.64

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX.

QtVolviewerV1.64.zip

Acknowledgements

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

Software team

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,