pipeline for the creation of surface-based averaged brain atlases anja kuß zuse institute berlin
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Pipeline for the Creation of Surface-basedAveraged Brain Atlases
Anja Kuß
Zuse Institute Berlin
1/30/2007 2/13
Pipeline for the creation of surface-based averaged brain atlases
Course• Motivation and related work• The pipeline• Applications• Conclusion and future work
1/30/2007 3/13
Pipeline for the creation of surface-based averaged brain atlases
Motivation• Goals in neurobiology
– Investigation of anatomical and functional neural network properties
– Analysis of learning and behavior
• Usage of insect brains– Small, easy to access– Already identified structures and neurons
• Population-based brain atlases– Spatial reference for relating data from different experiments– Facilitate visualization of neurobiological data
1/30/2007 4/13
Pipeline for the creation of surface-based averaged brain atlases
Related work• Human brain atlases
– Registration and averaging strategies: Guimond et al. 2000, Toga et al. 2001
– Processing environment: Rex et al. 2003
• Invertebrate brain atlases– Fruitfly: Rein et al. 2002– Honeybee: Brandt et al. 2005
Sequencing and adjustment of methods
Integration into one visualization platform: amira
Averaged brain atlas of the fruitfly, data from Rein et al. 2002
1/30/2007 5/13
Pipeline for the creation of surface-based averaged brain atlases
Pipeline - Overview• Imaging and preprocessing• Segmentation• Averaging• Surface reconstruction
Schematic overview of the pipeline for the generation of surface-based insect brain atlases
1/30/2007 6/13
Pipeline for the creation of surface-based averaged brain atlases
Imaging and preprocessing• Confocal microscopy of stained brains• 2x3 overlapping tiles, 80-100 slices of 512x512• Merging of tiles• First visualization via slicing or volume rendering
1/30/2007 7/13
Pipeline for the creation of surface-based averaged brain atlases
Segmentation• Creation of label fields dividing the brain into already
defined substructures (neuropils)• Support of manual segmentation
Segmentation of neuropils in the honeybee brain
Median calyx
Mushroom body
Lateral calyx
Pedunculus
LobulaMedulla
Cb
1/30/2007 8/13
Pipeline for the creation of surface-based averaged brain atlases
Averaging• Affine registration of all data sets to a chosen template• Non-arithmetic label averaging• Elastic registration of all data sets to the resulting
average and repeated label averaging
Unaligned label fields Result of affine registration Result of first elastic registration
1/30/2007 9/13
Pipeline for the creation of surface-based averaged brain atlases
Surface generation• Generation of non-manifold surfaces using a generalized
reconstruction algorithm• Simplification and remeshing• Tools for editing the surface
~ 100.000 triangles ~ 25.000 triangles ~ 25.000 triangles, remeshed
Surface-based averaged model of the honeybee brain
1/30/2007 10/13
Pipeline for the creation of surface-based averaged brain atlases
Refining the atlas
Bee brain with a selection of integrated neuronsNeuron (red) sticking out the atlas after affine registration, the fitted neuron is shown in green
1/30/2007 11/13
Pipeline for the creation of surface-based averaged brain atlases
Applications• Analysis of the olfactory system in the honeybee brain• Standard atlas of locust and moth brain• Atlas-based segmentation• Extension of the fly brain atlas:
– Averaging of thoracic ganglia– Integration of projections of the legs and wings– Integration of identified neurons
Atlas of fly thoracic ganglion with overlaid individual surface reconstruction
1/30/2007 12/13
Pipeline for the creation of surface-based averaged brain atlases
Conclusion and future work• Methods for the creation and extension of population-
averaged atlases from 3D image data of insect brains• Atlases facilitate scientific investigations
• Hierarchical brain atlases– Anatomical and functional hierarchies– Representation at various length scales
• Generation of statistical shape models
Thanks for your attention
1/30/2007 14/13
Pipeline for the creation of surface-based averaged brain atlases
Future work• Hierarchical brain atlases
– Anatomical and functional hierarchies– Representation at various length scales
• Generation of statistical shape models
Pe1 neuron and surrounding neuropils