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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