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Author: Harrison, JJ
Author: Turner, RJ
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Methods Article

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device

Joe J. Harrison2, Howard Ceri2, Jerome Yerly3, Carol A. Stremick2, Yaoping Hu3, Robert Martinuzzi4 and Raymond J. Turner1*

1 Department of Biological Sciences, University of Calgary. T2N 1N4. Canada.
2 Department of Biological Sciences and Biofilm Research Group, University of Calgary. T2N 1N4. Canada.
3 Electrical and Computer Engineering, Schulich School of Engineering, University of Calgary. T2N 1N4. Canada.
4 Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary. 2500 University Drive N.W., Calgary, AB T2N 1N4. Canada.

* To whom correspondence should be addressed: Raymond J. Turner, Department of Biological Sciences, University of Calgary. T2N 1N4. Canada. Phone: 403-220-4308. Email: turnerr@ucalgary.ca

Biol. Proced. Online 2006;8:194-215. doi:10.1251/bpo127
Submitted: September 06, 2006; Accepted: October 28, 2006; Published: December 19, 2006.

Indexing terms: Biofilms; Imaging, Three-Dimensional.


Figure 6 Enlarged

Fig. 6:

3D visualization of microbial biofilms using amira®. A. A 2D average of an image z-stack for a P. aeruginosa PA14 biofilm stained with AO and TRITC-ConA. B and C. Isosurface rendering of the 3D volume data sets for AO and TRITC-ConA, respectively, extrapolated from the image z-stacks used to create the image in panel A. D. The merged, isosurface rendered 3D volume data set for AO and TRITC-ConA. E to G. Volume rendering corresponding to the data sets presented in panels B to D. H. A 2D average of an image z-stack for a C. tropicalis 99916 biofilm stained with the Live/Dead® cell viability kit. I and J. Isosurface rendering of the 3D volume data sets for Syto-9 and PI respectively, extrapolated from the image z-stacks used to create the image in panel H. K. The merged, isosurface rendered 3D volume data set for Syto-9 and PI. L to M. Volume rendering corresponding to the data sets presented in panels I to K. O and P. The oblique view of the P. aeruginosa PA14 biofilm pictured in panel A visualized using isosurface and volume rendering, respectively. Q and R. The oblique view of the C. tropicalis 99916 biofilm pictured in panel H visualized using isosurface and volume rendering, respectively. Each 2D image panel or 3D model represents a square surface area of approximately 238 × 238 μm.

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