Visualization Tools for 3D Gene Expression Data in Drosophila

Gunther H. Weber, Cristian Luis Hendriks Luengo, Scott E. Dillard, Derek Ju, Oliver Rübel, Soile V. E. Keränen, Mark Biggin, Damir Sudar, and Bernd Hamann



It is intrinsically difficult to visualize complex gene expression patterns and morphology in 3D, especially at cellular resolution. As part of the Berkeley Drosophila Transcription Network Project (BDTNP), we are developing methods to overcome this challenge using images of whole Drosophila embryos. Specific tools under development permit 1) visualization of raw confocal microscopy data, 2) interactive control and verification of the image processing algorithms and 3) visual analysis of complex gene expression patterns.

By adapting novel volume-rendering methods to multi-channel confocal microscopy data, every single channel of an image stack is rendered independently by mapping brightness information to color and transparency information. Resulting colors are blended using user-specified weights, supporting seamless blending between channels, including the possibility to show all three channels simultaneously. Three-dimensional slicing and rotation tools make it possible to visualize an arbitrary cross-section from an image stack, and to explore the interior of an embryo.

Our volume visualization prototype has been combined with user interaction tools to support quantitative determination of the accuracy of the BDTNP's nuclear segmentation methods. Nuclei are rendered to include information obtained from a nuclear segmentation mask. It is possible to select individual nuclei interactively and identify falsely segmented objects. This work has already yielded significant improvements in segmentation accuracy.

The BDTNP's final 3D gene expression data is in the form of matrices or "point clouds" that describe nuclear positions and their associated gene expression levels. We are developing a point cloud visualization tool that will be offered as an effective means for the fly community to access and analyze 3D expression data from the BDTNP.


Additional Material


Gunther H. Weber
For further information concerning the BDTNP please consult the project web page.