Pipeline for the Creation of Surfacebased Averaged Brain

Pipeline for the Creation of Surface-based Averaged Brain Atlases Anja Kuß Zuse Institute Berlin 1/30/200714. 7. 2006

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 2/13

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 3/13

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 Averaged brain atlas of the fruitfly, data from Rein et al. 2002 Sequencing and adjustment of methods Integration into one visualization platform: amira 1/30/2007 4/13

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 surfacebased insect brain atlases 1/30/2007 5/13

Pipeline for the creation of surface-based averaged brain atlases Imaging and preprocessing • • Confocal microscopy of stained brains 2 x 3 overlapping tiles, 80 -100 slices of 512 x 512 Merging of tiles First visualization via slicing or volume rendering 1/30/2007 6/13

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 Median calyx Mushroom body Pedunculus Lateral calyx Cb Lobula Medulla 1/30/2007 Segmentation of neuropils in the honeybee brain 7/13

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 1/30/2007 Result of affine registration Result of first elastic registration 8/13

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 1/30/2007 ~ 25. 000 triangles Surface-based averaged model of the honeybee ~ 25. 000 brain triangles, remeshed 9/13

Pipeline for the creation of surface-based averaged brain atlases Refining the atlas Neuron (red) sticking out the atlas after affine registration, the fitted neuron is shown in green 1/30/2007 Bee brain with a selection of integrated neurons 10/13

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 11/13

Pipeline for the creation of surface-based averaged brain atlases Conclusion and future work • Methods for the creation and extension of populationaveraged atlases from 3 D 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 1/30/2007 12/13

Thanks for your attention 1/30/200714. 7. 2006

Pipeline for the creation of surface-based averaged brain atlases Future work • Hierarchical brain atlases – Anatomical and functional hierarchies – Representation at various length scales Pe 1 neuron and surrounding neuropils • Generation of statistical shape models 1/30/2007 14/13