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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:

  1. histological staining
  2. Confocal Laser Scanning
  3. cleaning and alignment of the series (stack) in Amira
  4. segmentation of structures, data reduction and vrml export in Amira
  5. volume/surface rendering of the stack in Imaris
  6. 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)

  1. histological staining
  2. hand-drawings of serial sections with camera lucida
  3. digitization of serial sections
  4. cleaning and alignment in NIH Image
  5. filtering, data reduction, surface rendering in IBM Data Explorer
  6. export to VRML format using Marvin Landis' and Christopher Kline's conversion modules
  7. detailing added in Cosmo Worlds
  1. histological staining
  2. data analyis and image construction using Biorad Confocal Microscope
  3. import, filtering, data reduction, surface rendering in IBM Data Explorer
  4. export to VRML format using Marvin Landis' and Christopher Kline's conversion modules
  5. detailing added in Cosmo Worlds
(Present Methods)
  1. histological staining
  2. data capture using Leitz Microscope/Sony DKC-5000 camera or Zeiss Axioplan 2/Axiocam
  3. alignment of sections using Adobe Photoshop on Macintosh or PC workstation
  4. import, filtering, segmentation of structures, data reduction, surface rendering and export to VRML using ZIB Amira on an SGI workstation
  5. adjustment of shapes, behaviors and lighting in Cosmo Worlds

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