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m3d

For information concerning availability of m3d, the application developed under this project, contact: christian.pettersen@basalmed.uio.no

Demonstration data sets for m3d

These data sets are prepared for testing and validation of m3d.

All data files - zip format

The demo files provided below are taken from a series of projects carried out in the Neural Systems and Graphics Computing Laboratory at the CMBN and Department of Anatomy, and in collaboration with multiple other laboratories in Europe and the US, as listed in the publications. All data are from material collected from experiments approved by national and international authorities, as documented in the individual research reports. In these experiments, neuronal tracers are placed in well defined parts of the brain. The tracers are taken up by neurons, the cells that create the wiring in the brain, and are transported along the nerve fibers. Thus, a tracer deposit may give rise to labelling of neuronal cell bodies or terminal fields of fibers at a distance from the deposit site. The tissue is cut into thin sections on a microtome and the sections are investigated in microscopes. Computerized data acquisition methods (Lillehaug et al., 2002) are used to record the distribution of the labelled elements together with information about boundaries of brain regions and the external contours of the brain. The serial section data, with point and line coding of the distribution of labelling and the brain regions studied, are submitted to a 3-D reconstruction procedure (Brevik et al. 2001; Leergaard & Bjaalie 2002) that brings together the information that separated by the sectioning.

We recommend the following more comprehensive background reading about axonal tracing, provided by the laboratory of Larry Swanson at The University of Southern California, USA: A Theoretical Approach to Systems Level NeuroAnatomy. http://chasseur.usc.edu/ns/documentation/theoreticalapproach.html

References:
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; 204:319-32 (Special issue: Computational neuroanatomy -- Tools for single neuron, system, and brain region analysis, ed. J.G. Bjaalie).
PDF of this article, Link to publisher

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

Monkey cerebral cortex (xpa format)
3-D reconstructions of serial sections through large parts of the monkey brain, showing, the external contour lines of the cortex (external_contours), a large population of neuronal cell bodies labelled with the use of axonal tracing techniques (neurons), and multiple boundaries and landmarks that serve to identify location parameters in the reconstructed tissue. The cell bodies are labelled following large axonal tracer injections into the brain stem pontine nuclei. They represent the cells of origin of one of the largest systems in the brain: the pathways from the cerebral cortex onto the cerebellum.

For details see:
Vassbø K, Nicotra G, Wiberg M, Bjaalie JG
Monkey somatosensory cerebro-cerebellar pathways: Uneven densities of corticopontine neurons in different body representations of areas 3b, 1, and 2.
J Comp Neurol. 1999; 406:109-128.

external_contours_cx - outlines of the external surface of the brain
neurons_cx - points representing labelled neurons
sulcus_cx - reference points at the bottom of the central sulcus of the cerebral cortex
a4_cx - boundaries between cortical areas
b1_cx
b2_cx
b3a_cx
b3b_cx
b4_cx

Rat cerebellum (pa format)
3-D reconstruction of the surface of the rat cerebellum, based on serial sections. The reconstruction is divided into 8 separate files, to be viewed simultaneously.

For details see:
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; 204:319-32 (Special issue: Computational neuroanatomy -- Tools for single neuron, system, and brain region analysis, ed. J.G. Bjaalie).

cerebellum_1a - outlines of the cerebellum
cerebellum_1b
cerebellum_1c
cerebellum_1d
cerebellum_2a
cerebellum_2b
cerebellum_2c
cerebellum_2d

cerebellum.j3d - m3d universe file

Rat pontine nuclei (xyz format)
3-D reconstruction of the ventral brain stem (ventral_surface), the descending fibre tracts (peduncle_*), the pontine nuclei (pontine nuclei_*), and the distribution of labelled axonal terminal fields (filnavn….) within the pontine nuclei. The labelling data represent terminal fields of axons originating in individual barrels (whisker representations) of the somatosensory cortex. These terminal fields contact cells is the pontine nuclei projecting to the cerebellum. The data demonstrate aspects of the map transformation from the cerebral cortical level to the brain stem (precerebellar) level.

For details see:
Leergaard TB, Alloway KD, Mutic JJ, and Bjaalie JG: Three-dimensional topography of corticopontine projections from rat barrel cortex: Correlations with corticostriatal organization. (J Neurosci 20:8474-8484, 2000)
and http://www.nesys.uio.no/Database/2-SIwhisker-PN/

Unaligned sections
Aligned sections
Model

rat_pontine_nuclei.j3d - m3d universe file