3D Reconstruction and VRML Export of Confocal Image Data

  The Fischbach laboratory, University of Freiburg, uses Laser Scanning Confocal Microscopy as a standard technique for visualization of mutant and wildtype structures of the larval and pupal Drosophila melanogaster nervous system. Series of confocal images are used as datasets for three-dimensional reconstruction using the developmental 3D visualization software AMIRA from the Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) as well as Imaris (Bitplane AG, Switzerland) on SGI workstations.

  Three-dimensional and interactive models can be made available on the internet for normal desktop computers using the Virtual Reality Modeling Language (VRML).
VRML is a 3D description language that allows interactive programming using VRMLScript, JavaScript, or Java in the VRML version 2. This version has become an ISO standard (ISO/IEC 14772) under the name VRML97. Thus, VRML is momentarily a reliable language to present 3D data. Browsers (plug-ins for Netscape or Internet Explorer) are freeware and available for PC, Macintosh and UNIX platforms:

Cosmo Player, Cosmo Software, SGI
        (PC, Mac, Silicon Graphics)
WorldView, Intervista
        (PC, Mac)

  The VRML97 model presented here is a three-dimensional reconstruction of a pupal (P+75%) Drosophila optic lobe and part of the central brain, i.e. roughly half of a complete Drosophila brain.
The reconstruction bases on a antibody staining against the cell adhesion molecules irreC-roughest. More information about this can be found on the homepage of the Fischbach Laboratory.
The original dataset consists of 182 images with 512x512 pixels. The size of the virtually cut out part of the brain is 100um * 250um * 250um.

  Once you have installed one of the suggested plug-ins, you may now investigate the model. The reconstructed 3D VRML97 model consists of 10 surfaces (objects) consisting of several thousand triangles. Furthermore, nearly 100 images (converted original confocal images (z layer) as well as interpolated images (x, y layers)) can be moved through the 3D volume. Additionally, all surface objects can be removed. By clicking onto the surfaces a little ball appears next to the y bar instead of the surface. You may click on these little balls and the surface reappears.

VRML97 IrreC-rst Optic Lobe of Drosophila melanogaster
        (1 MB data, 100 files)
  Scientific information:
The staining with an antibody against the molecule IrreC-rst shows major parts of the neuropils of the optic lobe, i.e. structures where synaptic arborizations are located. At the developmental stage (75% of pupal development) of this specimen, the staining does not show any fibers or cell bodies of the optic lobe or central brain. The antibody or other staining method one uses actually are the glasses through which one looks at the anatomical structures one wants to see. In the reconstruction presented here, the following structures of the Drosophila brain are visible:
  1. grey/blue (slightly transparent): Lamina
  2. major purple structure: Medulla
  3. yellow structure: Lobula
  4. orange structure: Lobula Plate
  5. transparent grey: part of the central brain
  6. coloured small structures within the central brain: optic foci
  Volume rendered optic lobe (IrreC-staining, same dataset as above; mab nc82 antibody staining) :
In contrast to the surface rendered VRML2 model described above, volume rendering allows to use algorithms like raytracing to produce realistic recontructions of confocal data. Volume rendering takes more time than surface rendering (sometime much more - depending on the algorithm). Real-time volume rendering can be performed with the software Amira described above. Here, we provide a movie of volume renderend views of an optic lobe. Staining: mab nc82 (unknown antigen, neuropil marker, Hofbauer library), image stack acquired with the confocal microscope (same size as IrreC specimen).
IrreC-rst (same dataset as VRML), Quicktime Version (2.2 MB)

nc82 staining; Quicktime Version (1.6 MB)
nc82 staining; MPEG Version (1.8 MB)

For more information about the anatomy of the Drosophila nervous system and the function of the IrreC-rst molecule, as well as more 2D and 3D data please consult the FLYBRAIN database.


3D Experimental Site | Related information: VRML2 reconstruction of the Antennal Lobe, Peter Robin Hiesinger, 1998-1999