biomedical atlas centre
TRANSCRIPT
PowerPoint Presentation
ELIXIR-UK: Biomedical Atlas Centre
the UK Node of the
Richard Baldock, Dave Burt, Albert Burger, Susan Lindsay, Alan Archibald
European Life Sciences Infrastructure for Biological Information
www.elixir-uk.org
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Why an atlas?
Organism & tissue level framework for spatio-temporal data collate, compare, analyse
Knowledge repository anatomy, definition of terms
Dumb image coordinates to anatomy/histology/biological space
Framework for interoperability individuals, species, development
Framework for systems modelling
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Biomedical Atlas Centre
University of Edinburgh
IGMM Richard Baldock
Roslin Dave Burt, Alan Archibald
Newcastle University
IHG - Susan Lindsay
Heriot Watt University
CS - Albert Burger
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emouseatlas.org
hudsen.org
echickatlas.org
gudmap.org
eurexpress.org
macs.hw.ac.uk/bisel/
Mouse Atlas emouseatlas.org
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Kaufman reference specimens or holotype
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Mouse Atlas emouseatlas.org
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Chick Atlas echickatlas.org
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Atlas to HH stage 26
2K Gene-expression assays
HuDSeN hudsen.org
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B-cat Reporter
Atlas Informatics
ELIXIR Themes Data
Spatially & anatomically mapped gene-expression data
~37K in situ assays, ~400K images
~ 5K sample based assays microarray & RNA-seq
Atlas Models & 3D datasets
Developmental sequence 3D models, mouse, human, chick
Atlas models most stages mouse, human, chick
Full 3D human data-sets 100 normal, 75 abnormals
High-resolution Histology & Ontology
Histology series/atlases mouse & human embryo, mouse placenta
Developmental anatomy ontologies for mouse & human, beta-anatomy for chick
Data sets published with DOIs & in DataCite
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ELIXIR Themes Tools
3D reconstruction & anatomy delineation applications
complex 3D spatial mapping (constrained distance transform)
high-performance image processing for pattern comparison and analysis (woolz C, Java & python)
Data-structures for complex mesh-based transforms
3D tile-server tools for very large image data (100GB+)
Web-based visualisation tools & interfaces (MARender)
DB & web-application for 3D spatial data.
All open-source matech on GitHub
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ELIXIR Themes Compute
Web-servers for spatial data - dynamic spatial comparison & sorting
Web-services for gene-expression, atlas data & DB query
3D image tile-servers, arbitrary re-sectioning
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ELIXIR Themes Interoperability
Ontologies linked through Uberon & direct mappings mouse-human-chick
spatial-mapping services (beta)
DAI implementation for Waxholm space (INCF)
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ELIXIR Themes Training
Training courses
Online videos etc
Online anatomy teaching materials
Model meshes for 3D printing (HuDSeN)
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Future
Biomedical Atlas Centre
Convergence of systems common software tools
Build on infrastructures e.g. OMERO
Develop interoperability standards
Implement ELIXIR services & Integration
Web-based tools for 3D image data browsing & visual-analysis
Atlas hosting other species
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Biological direction the missing part
Biological Directions in image space
left-right
dorsal-ventral
anterior-posterior
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End
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