Micro3D

www.nesys.uio.no


 


Welcome to the Micro3D user group

As a member of this user group, you have access to the Micro3D 2004 software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions, on the conditions specified on the donwload page. Extensive user manuals and tutorials are available. Further assistance with the use of Micro3D is provided via the user forum.

Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level.

Micro3D 2004 generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos.

Micro3D 2004 and forerunners have been developed by the Neural Systems and Graphics Computing Laboratory (NeSys) with support from The Research Council of Norway and The Oslo Research Park / FORNY. NeSys is currently developing similar software based on Java3d. This software will be platform independent and will also contain novel features that are not covered by Micro3D. Comments received by users of Micro3D will be constantly used to influence the development of the new Java3d based software that will later be released for members of the present user group. We encourage all users to make active use of the forum and place comments and questions related to the present version of Micro3D.


The Micro3D project is directed by Jan G. Bjaalie, Neural Systems and Graphics Computing Laboratory, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1105 Blindern, N-0317 Oslo, Norway.

Webmaster and Micro3D development: Dmitri Darine

Micro3D references

Recent references:


Zaborszky L, Csordas A, Buhl D, Duque A, Somogyi J, Nadasdy Z: Computational anatomical analysis of the basal forebrain corticopetal system. Computational Neuroanatomy: Principles and Methods (ed. Giorgio Ascoli). 2002; pp. 171-197. Humana Press: New Jersey


Leergaard TB, Bjaalie JG: Architecture of sensory map transformations: axonal tracing in combination with 3-D reconstruction, geometric modeling, and quantitative analyses. Computational Neuroanatomy: Principles and Methods (ed. Giorgio Ascoli). 2002;
pp.199-217. Humana Press, Totowa NJ.


Brevik A, Leergaard TB, Svanevik M, Bjaalie JG: Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualisation, and comparison of spatial distribution data. Anat Embryol. 2001; 319-332 (Special issue: Computational neuroanatomy).