Three-dimensional Reconstruction of the Drosophila Larval and Adult Brain
|Help Index Where Am I? Search Page Status||Contact Us|
Confocal microscopy and 3D Reconstruction: A Leica TCS4D confocal microscopes equipped with an ArKr-laser was used for data acquisition. Series of complete optic lobes were scanned with a 40x objective (aperture 1.0) and comprised 182 images of 512x512 pixel resolution at 8 bit color depth (47MB for each channel). The data were three-dimensionally reconstructed on a SGI Octane MXI graphics workstation using the 3D visualization software Amira (Konrad Zuse Zentrum, Berlin). Brain structures were demarcated by hand in confocal image stacks to define labels for the different structures, thus producing polygon groups of the surfaces of the structures. The polygon data were exported to the Virtual Reality Modeling Language (VRML 2.0 utf8). The resulting surface models were further processed with Cosmoworlds (Cosmosoftware) and optimized for smooth handling on current desktop systems. Volume rendering for the movie was performed with the software Imaris from Bitplane (Switzerland).
Confocal microscopy: Optical sections were acquired using a Leica TCS-NT confocal microscope equipped with Leica objective lens with a numerical aperture of 0.7. We measured an axial resolution of about 2 µm for this setup. According to the sampling theorem we chose to sample at about 1 µm in all directions, thereby accepting an undersampling in the lateral plane (as the lateral resolution is better than 2 µm). This resulted in image stacks with a size of 535 µm x 535 µm x 195 µm, or 512 x 512 x 168 voxels respectively (about 42 MB).
Data analysis: All data analysis and visualization were done using the Amira Software (Konrad Zuse Zentrum Berlin, http://amira.zib.de) on graphics computers (Indigo 2 High Impact, Onyx2 Infinite Reality, Silicon Graphics). Brain structures were labeled manually with the help of interactive tools. Surfaces were generated and exported into the VRML format. The image data were resampled into a standard orientation (frontal plane parallel to the ellipsoid body plane). Volume rendering for the movie was again performed with the software Imaris from Bitplane (Switzerland).
Main | The Flybrain | About 3D Reconstruction | Handling of 3D Models | References
Return to Flybrain 3D Models
|Flybrain Atlas Dissectable Brain Materials and Methods|
All contents are copyright © 2000 Flybrain or their original publication (as noted).
Copyright and use policy
AB00126Page last modified: July 24, 2000 by Managers.