Biomedical Atlas Centre

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Introduction to the ELIXIR-UK Biomedical Atlas Centre presented by Richard Baldock at the ELIXIR-UK Workshop during Genome Science 2016 in Liverpool on 31st August 2016

Science

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
2

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
3
emouseatlas.org
hudsen.org
echickatlas.org
gudmap.org
eurexpress.org
macs.hw.ac.uk/bisel/

Chick Atlas – echickatlas.org
6
Atlas to HH stage 26
2K Gene-
expression assays

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
9

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
10

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
11

ELIXIR Themes – Interoperability
• Ontologies linked through Uberon & direct mappings
mouse-human-chick
• spatial-mapping services (beta)
• DAI implementation for “Waxholm” space (INCF)
12

ELIXIR Themes – Training
• Training courses
• Online videos etc
• Online anatomy teaching materials
• Model meshes for 3D printing (HuDSeN)
13

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
14

Biological direction – the missing part
• Biological Directions
in image space
• left-right
• dorsal-ventral
• anterior-posterior
15

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1. European LifeSciences Infrastructure for Biological Information www.elixir-uk.org ELIXIR-UK: Biomedical Atlas Centre the UK Node of the Richard Baldock, Dave Burt, Albert Burger, Susan Lindsay, Alan Archibald

2. 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 2

3. 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 3 emouseatlas.org hudsen.org echickatlas.org gudmap.org eurexpress.org macs.hw.ac.uk/bisel/

4. Mouse Atlas – emouseatlas.org 4

5. Mouse Atlas – emouseatlas.org 5

6. Chick Atlas – echickatlas.org 6 Atlas to HH stage 26 2K Gene- expression assays

7. HuDSeN – hudsen.org 7

8. 8 B-cat Repor ter Atlas Informatics

9. 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 9

10. 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 10

11. 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 11

12. ELIXIR Themes – Interoperability • Ontologies linked through Uberon & direct mappings mouse-human-chick • spatial-mapping services (beta) • DAI implementation for “Waxholm” space (INCF) 12

13. ELIXIR Themes – Training • Training courses • Online videos etc • Online anatomy teaching materials • Model meshes for 3D printing (HuDSeN) 13

14. 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 14

15. Biological direction – the missing part • Biological Directions in image space • left-right • dorsal-ventral • anterior-posterior 15

16. 16 End

Editor's Notes

Kaufman reference specimens or holotype

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