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Welcome to Ogles2

Ogles2 is an interactive slice and volume visualization and analysis tool based on Open Inventor / Coin3D. Ogles2 allows for reproducing the workflow of frame based stereotactic neurosurgery. In the long run it strives for being an open source stereotactic planning and analysis system. Ogles2 is NOT APPROVED FOR CLINICAL USE.

Ogles2 main focus is to combine slice derived volume data with surface meshes in the context of stereotactic neurosurgery. Recent development was driven by the attempt to transform 3D brain atlas data to individual brain configurations and to estimate the effects of electrical fields of deep brain stimulation (DBS) electrodes. Ogles2 is in the beta phase.

Ogles2 utilizes a large amount of code from other projects, which are published under different terms of license. Please refere to the 'About' page. Ogles2 itself is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

Ogles2 is accompanied by a simple Dicom reader (Sdr2), yet another Dicom to NIfTI converter.

  • Import of Nifti, Analyze, and *.vol (Barthold Lichtenbelt, 1998) data files
  • Spatial information from Nifti files considered
  • Import of Open Inventor (.iv) and VRML (.wrl) files
  • Volume rendering
  • Polygon based manual segmentation and surface mesh construction
  • Transformation of 3D surface models (9 degrees of freedom)
  • Setting of AC-PC based coordinate system
  • Semiautomatic rod detection for ZD and RM localizers
  • Definition of trajectories
  • Simulation of DBS lead (Medtronic No. 3389) and electrical fields
  • Visualization and quantification of electrical field and geometry model intersections
  • Limited coregistration of volume files
  • Isosurface calculation
  • Transformation of surface meshes to AC-PC system:

    If an inventor file (*.iv) has a header entry like:

    #Inventor V2.1 ascii

    #III. ventricle length = 23.2 mm, width = 1.8 mm

    #File AC: 0.0, 11.6, 0.0

    #File PC: 0.0, -11.6, 0.0

    #File MPP: 0.0, 0.0, 20.0

    then Ogles2 will transform 3D geometry into image AC-PC coordinate system.

    Limitations / missing:
  • Not all bugs fixed (beta phase)
  • Stereotactic planning not sufficiently tested
  • Rod detection needs careful windowing and is limited to ZD and RM localizer systems
  • Weak coregistration
  • No painting
  • Manual segmentation only
  • Saves path to images, AC-PC coordinates, and trajectory data only
  • No documentation provided
We are looking for collaboration to evaluate and improve our data model,
please contact us with any feedback.