The Flybrain 3D-Project Methods

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Methods

Within the collaboratoration for Flybrain, projects for developing VRML models have evolved seperately in Freiburg and Tucson. Along with developing both idealized structures and a collection of anatomical models, differences in the models come from the software and hardware available at both sites.

Fischbach Laboratory methods (Freiburg, Germany)

The Fischbach laboratory 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 highly specialized program Imaris, which supports data-export into the VRML 1.0 format. The goal of our work is to make the technique of 3D-reconstruction of microscopic preparations as simple as the routine of producing 2D-images.

Construction of the models requires the following steps:

histological staining
Confocal Laser Scanning
cleaning and alignment of the series (stack) in Amira
segmentation of structures, data reduction and vrml export in Amira
volume/surface rendering of the stack in Imaris
refinements with Photoshop for SGI (pics) and Cosmoworlds (VRML)

Hard- & Software used:

We are working with a Confocal Laser Scanning Microscope System (TCS4D) from Leica for data production.
Structure demarcation, reconstrution and VRML export are done with ZIB Amira. Volume rendering is done by the Imaris & Selima package from Bitplane AG, Switzerland. Movies are edited with SGI Multimedia processing software and VRML is edited with Cosmoworlds. As browsers we use Netscape 4.7 on SGI workstations.

Strausfeld Laboratory methods (Tucson, USA)

Construction of the models requires the following steps:

(Past Methods)

histological staining

hand-drawings of serial sections with camera lucida

digitization of serial sections

cleaning and alignment in NIH Image
filtering, data reduction, surface rendering in IBM Data Explorer
export to VRML format using Marvin Landis' and Christopher Kline's conversion modules
detailing added in Cosmo Worlds

histological staining
data analyis and image construction using Biorad Confocal Microscope
import, filtering, data reduction, surface rendering in IBM Data Explorer
export to VRML format using Marvin Landis' and Christopher Kline's conversion modules
detailing added in Cosmo Worlds

(Present Methods)

histological staining
data capture using Leitz Microscope/Sony DKC-5000 camera or Zeiss Axioplan 2/Axiocam
alignment of sections using Adobe Photoshop on Macintosh or PC workstation
import, filtering, segmentation of structures, data reduction, surface rendering and export to VRML using ZIB Amira on an SGI workstation
adjustment of shapes, behaviors and lighting in Cosmo Worlds

Flybrain Atlas 3D Flybrain 3D Methods

AC00105