OME:
An Open Image Informatics Solution for Biological Microscopy
Jason Swedlow
Wellcome Trust Biocentre
University of Dundee
Dundee, Scotland j.swedlow@dundee.ac.uk

Jigna
Patel
Ana
Amores
Paul
Andrews
Elena
Knatko
Markus
Posch
Guennadi
Khoudoli
Iain
Porter
Andrea
Falconi
Jean-Marie
Burel
Chris
Allan
Arwen
Wilcock
Mairead
Murnion
Melpi
Platani
Karen
Duncan

An Informatics Continuum
GAATTCCCAAATCAAGGAGAGATACTTAGACCTAGCTAATAGCGACAGGATGAGGTTCAAAACTCTCCTTTTTAAATGATGACTAAAATAAAGACAATCGAAAGAAAAAATACATAGACAACAAAACCACAA
GAAGATGAAGATGGAGGAGGAAGGCAAAAAAGTGCCAGCAAGCTGGGTGTGGTGGTAAACAGTAATGCTAGAACTTGGGTGAAGGATCAAGTTGTCTAGGCCATTCATTGCAGGAAAAGTTATTTTCCTATT
TTCAGTCACAAAGTGAGCTCACATCCCCTTCACCTGTGCTCTCAAACTGTCACTGCTTCACCCCAAAATTGTAGCAGCTTTCCTCAATCTGCCTACACTGGCCAATCACATTAACAAAAATCAGACTACAGG
AAGCTATTCCAAGAACACCCCTGCCTTTACCAACCTTGGCCACGGGGTGAAGCTGTAAAGGGGGTCATGAAATGGAAGCTACTATACTTACACGGCATTAGAGTTCTCAAATACAATGCCATTTATCTTAGT
TGTGTAATCACCATGTTAAGACATGAATCCGCTGGGACTCTGCCTGTTCTGAGAAAGAGAAACAAAACAAAACAAAAAACAATTTTTGCCATTGCATTGTTGGCAAAAAGGCCACATCTCAGGGCAAATGGT
TGAGAATTATGAGGAATGTTTAGTTCTGCCTTACATGGACTTTACTTGAACCCCGCCCGGACTTACAGACGTTTTTAATGTGGTTAGATGAGAACCATGCTTAACTGCTTTCCTATCCCTCACTCAGGCTTT
CCTCAAGGAACAGAGTTTAGCTGCGCACACTTAATAAGGCAGTATTTCTTTTCCAAGAAAATGGTGCAAACTTGACCTTACAATTCTCCAAAGGCACTCAAGGTTTATTTACTCAATTTCTCTATATTCTCT
GAGATGCCCAAGCTGTTAAGTGGTTCAGTATTACAGCGCTTTTTCAGGGAATGTGGGCGGCCCTGAGAAGGGCCTTTGGTTAGAAAATACAAATTAAAAAAGTCTTAGCCGCCGAATCCGTAGAGGGTGCGG
CCCTGGCGCTTGAGCGCGTAGACCACGTCCATGGCGGTGACGGTCTTGCGCTTGGCGTGCTCCGTGTAGGTGACGGCGTCGCGGATCACGTTCTCCAGGAACACCTTCAGCACACCGCGGGTCTCCTCGTAG
ATGAGGCCGGAGATGCGCTTCACTCCCCCGCGCCGGGCCAGGCGGCGGATGGCGGGCTTGGTGATGCCCTGGATGTTATCGCGGAGAACCTTACGGTGGCGCTTAGCGCCGCCTTTGCCCAGGCCTTTTCCT
CCCTTGCCGCGACCCGACATGTCTTAGGAAGAATGGAAAATGGAGTCAGAGCTGAGAGTCGGTCCTTTATATAGCTGCTTGGCCTTGATCTCCCACCCCCAACAGAATCACACAAACGAAAACCCGCCCGCC
GGACGGTGACGTCATAAACCCCGCCAATAAGACCTGGCGGGAAAGAACCGAAAGCGCCCGGGCGGGAAAGTGACGTCACAAATCCCTCCCATCAACCATGCCCCGAAAGCGCGCCGGCGGGAAAATGACATC
ACAAACCCCGCCCCTCAGCCAAGACCCGAAAGCGCGCCGGCGGGAAAGCGACATCAGTGATCCCTCCTCTCAGCCATGCCGGGAAAGACGCAAAAGCCCGCCGGCGGGAAAGTGACTTCACAAATTCCGCCC
CTCAGTCACGACCAGAAAGCGCGCCGGCGGGAAAGTGATGTCACATATCTCGCCCATCAGCCCCGCCCCGAAAGCCGGACGGCGGGAAAAGTGACATCACAGACCCCTCTCTGGATCGGAGCCCTTTAAGGA
CCGAAAGCCTGCGAGCAGGTCACGTCAGAGATCCGACCCGTACATTTTACGCATATTCCACGGGTAAAACCAGACACTCAGTTGACCTATTTTGTACTTGATATCAACTTTGGGCTGTTATAAACTCAAGTT
TTGGGGAATATCCACCGTTATAGACACTAGGGAACATATAGGTTCGTTTAAGGATGGAGTAAATTACAGCCATTTTACTTGAAATCGTGTGTGGCTCTGAAAAGAGCCTTTGGTTAATTCCGTAGAACTGTA
CGGAACTGTACAATTACGCCCTCTCCCCGCGGATGCGGCGGGCCAGTTGGATGTCCTTGGGCATGATGGTGACACGCTTGGCGTGGATGGCGCACAGGTTGGTGTCCTCAAACAGACCCACAAGGTAGGCCT
CACAGGCCTCCTGCAGAGCCATGACGGCCGAGCTCTGGAAGCGCAGGTCGGTCTTGAAGTCCTGCGCGATCTCGCGCACCAGGCGCTGGAACGGCAGCTTGCGGATCAGCAGCTCGGTCGACTTCTGGTAGC
GCCGGATCTCGCGCAGCGCCACGGTGCCGGGACGGTAGCGGTGAGGCTTCTTCACGCCGCCGGTGGCCGGGGCGCTCTTGCGGGCGGCCTTGGTAGCCAGCTGCTTACGCGGGGCCTTGCCACCGGTGGACT
TGCGAGCGGTCTGCTTAGTACGAGCCATAGCAAAAACTAGAAAGCAAGCGGGTGAGCACTTGGAGATGGTGAGTTCAGAACTACTATTTATAGTATGCAAAGGATAGTGATTGGATGAAAATACTGGTTATC
TGTGACGTTTAAGACTCTGATTGGTTTATGTTTAAGAACTGCAGTTGAGGCTAAGGTAGTCTGCCGCGGTACTTATTTTTGTATGTGTGTGTTTTAAAGTAAATGGAATAAAATTCCAGTGACTGTTATCTT
CTACAGCACATCTGCTTCCAAACACATTGCAGCTTGAACTTAGTGGCATTGAAGAATAGAGAACAATCTTGTTATCTTCATTATTGAAATGTAAGAATGTGACTTCTACATTGAAGGAGAGTAGGCCAGATT
CTACCTTTTGATTGGTTTACTGCCTTTCGTAAATAGCCACTAAAACAGCAGATTTAGAACTCTTCATTTGCGTGGAAAGTCTCCATTTTGTTGCAACCCACACTGTAAAGAAATGGAGAGAAACATGGGAGT
AAAAGTTACAGACGTCTGACTCGGGTTATTCTGAGCATTTCTTCATTAAATGGCTGTACTTGTATGGATGCTTTCAGTTCTTGCATTTGGAGCTTGAATTTTCAAAATACTTTCACGCATTTTTGGCCAGAT
ATCACTGATACGTTCGAAAACAATTTTTTAACTATAAACTATAGAAATCGTCATAGCATGTTAGGATTGCACTTTTAAATTCTTTTAAAAAAAAAAATGGGCAAGACTTTCCCAGAGCTATTGTGTACTTGC
ATATCCTGGGAAAAGTCGTGTCCTGCCTTTTCTCTTTTTATTTGAGCCACTACTGGCTCACAATATGAAATCACTGTCGCAAGCTGACACTCCTTAAAAGAACACTAAGCCTCTTGCATAACTAATATATAA
AGTAACGATACATTGCTCCCATTACTGCCAAGAATCAATACTGAAACCCGCAGAGAAGGCCCACAAGCTGGCTTTCTGGGTTTTAATTGACTAATTTACAGCCACCTTTCACTAGTTGAGCTCCTTTTTGAT
AGGCATCTACCACTTTCTGATGATAAAACAGGAGAGTACAAGGAGAATCTGCTGTGGTTGAAATTCCACCTCAAGCAGCCAGCCGGAGAAGTTTTGAGGCCGCCTCCTCTACCTGCAAAAACACGAAGCTAG
GTCGGTGGAATCGCAAAGGAGTTAGTTTCTGAAATCTTGCAGGCAGACAGGCGCACGGGAGGCGGGGCCTTAGGGTCCAGGGGGCGGGCGTTAGCATTCACCAATCACAGCACAGCACTGCTCTATAAATAC
TCCGTGCAGGGGCCTTGTCTTTCTACTTCTTTTCTTCGTCTTGGGTATAGCTGTTGTTTATTCATCAGCGACCATGTCGGAGACGGCGCCAGTCGCTCAGGCTGCTTCTACTGCCACGGAGAAACCTGCTGC
TGCAAAGAAGACCAAGAAGCCGGCAAAAGCTGCCGCTCCTCGGAAGAAGCCCGCGGGACCTTCGGTGTCGGAGCTCATCGTGCAGGCAGTTTCTTCTTCCAAAGAGCGCAGTGGCGTGTCCTTGGCCGCGCT
CAAGAAGTCGCTGGCTGCGGCGGGATACGATGTGGAGAAGAACAACAGCCGCATCAAACTGGGGCTGAAAAGCCTGGTGAATAAAGGCACACTGGTGCAGACCAAGGGCACCGGCGCTGCTGGCTCTTTTAA
GCTGAACAAGAAGGCTGAGTCCAAGGCCATCACCACCAAGGTGTCAGTGAAGGCGAAAGCATCCGGGGCTGCTAAGAAACCTAAGAAGACTGCTGGGGCTGCAGCTAAGAAGACTGTCAAGACTCCGAAGAA
GCCCAAGAAGCCTGCAGTTTCCAAGAAGACTTCCAAGAGCCCCAAGAAGCCGAAGGTGGTGAAGGCCAAGAAGGTAGCCAAAAGCCCTGCCAAGGCGAAGGCAGTGAAGCCTAAGGCTTCCAAGGCGAAAGT
GACAAAGCCAAAGACCCCAGCTAAGCCCAAGAAGGCAGCGCCCAAGAAAAAGTGAACAGTTGGAGGCTTCTTCTATAACCCAACGGCTCTTTTCAGAGCCACCAACATAACTCAAAGAGCCTGACACTTGTT
TCACACTATAACAACTGCATTTGGGTACAAGCCTGGTGGGATTTAGGCATTATTAATTTCCCCCAGTAAACTGACAATTTGGGTCAGTCTAGTTTCTAGTTTTATTTCCCTGAGATTCTGGGAAAACAGCCT
TGTTAGCCCTGGGAGGCGCTACCCTCTCCAGGTGTGGTGGATAAGCTCTCTATGGTATGGTAGTGCAATGGCCTGGGTGCCTCAACCAGATAAGGTCCTATTTTGCCAATGAGGATGAGAACTCAGGTGCTT
GATCAGTAAGAGTGGGCTGCAGCAAGGGTTCACATGCAATAGAGTTTTTTTTGTTTGTTTTTTTAGGGGGGGGGGGGCCGAGACCGGTTTCTCAGTGTAGCCCTGACTGTCCTTGAACTCACTCTAGACCAG
GCTGGCCTTGAACTAAGAAATCCGCCTGCCTCTGCAGTGCTGGAATTAAAGGCGAACGCCACCACGCCCGGCTGCAATAGTTTTTTTAATTCAAGCCCACCAAGACTGTTCCTTACAGGAATGCTAGGTGCT
TGGAGGCTTGGTTTTGTGAGGAAGTGGTTATCTCCCATGTACTGCAATGTTCACAGGCAGCTCTTGAAGCCTTTATTGATTTTTGCTAAGTAGCCACTTTTGTCCCTGCATTGATCCTCCTTCCTCCAAAGA
GCTAGAGTTAACGCCCCACACCGTGATTTGCTGGGCTCCCTTATTCTGAGCTCAGTTTTTAAATTATTGGGGGTGGGGGGATTGTCTGGAAGTTGAGGGGCAACTTGAAATTGGTTCTCTTCCACTACTTGA
GTCCAGGAGACTAGTTAAAGTCATCAGGCTTGGCGGCAAGTTCCTCTTACTCTGAGTGTCTTCTGGCCCTGAATTTAACTTTGTTGTCCTCTTTCAACAAAAAATTAGAAAACCAAGTGTCTGAGGCGATTG
GCCTGTTATCTCAAGTACACAGGAGGCCAAAGTAGTTTGGACTTCCTGAATTC

An Informatics Continuum
Live HeLa Cell
GFP-coilin
YFP-histone H2B
Platani et al (2002) Nature Cell Biol. 4:502-508

An Informatics Continuum
25
20
15
10
5
0
-3 -2.6 -2.2 -1.8 -1.4
-1 -0.6 -0.2
0.2
0.6
1 1.4
1.8
2.2
log D
Log D
Control (N = 250)
Sodium Azide (N = 103)
Platani et al (2002) Nature Cell Biol. 4:502-508

Image Informatics-- The Dirty Laundry
Ctrl Sodium Azide

Towards Image Informatics

Towards Image Informatics
Experiment-
Cells
Experiment-
Protocol
Acquisition
System
File-
Structure
File-
Image
File-
Display
Processing--
Images
Processing--
Results
Processing
History
Measurements Tracking ……

• Store images, metadata, and analytic results in a
single relational database
• Make an interface for easy access from desktop
for processing and analysis
• Apply query and mining tools on database for discovery
• Discovery and analysis of cellular structure & dynamics
• Cell-based HTS of small molecule libraries

Open Microscopy Environment
• Relational database for digital microscope images &
informatics
• Open system that specifies database architecture
& interface
• Designed to promote platform & package
independent access to data
• Open source code (modeled after Linux; licensed
under LGPL)
• Allows database mining and querying
• Promotes IP for digital image screening and informatics http://www.openmicroscopy.org

OME Academic Collaborators:
Jason Swedlow, University of Dundee
Peter Sorger, MIT
Ilya Goldberg, NIH
Erik Brauner, Harvard Medical School, ICCB
Gaudenz Danuser, ETH Zurich
Commercial Partners
Applied Precision, Inc.
Universal Imaging, Corp.
Carl Zeiss Vision, Inc.
Olympus, Inc.
Improvision, Inc. Leica Microsystems
Chroma Technology Corp. Omega Optical
Intelligent Imaging SVision, LLC
Innovations, Inc.
http://www.openmicroscopy.org

OME-- An Image Informatics Solution!!!!
Visualisation
Querying
Open source
Wrapper
API
Acquisition
Transformation
OME
Storage
Analysis http://www.openmicroscopy.org

Nuclear Import Screen: Yan Feng, Harvard ICCB

• Successful integration of acquired image data,
analysis and relational database
• Use of querying tools for analysis of images from
time-lapses studies and cell-based screens
• Established use of relational database as interface
between proprietary files and legacy code http://www.openmicroscopy.org

• XML File Schema:
http://www.openmicroscopy.org/docs.html
¸ Image data (pixels)
¸ Metadata (acquisition info, image stats, etc.)
¸ Complete transformation and analysis history
Swedlow et al (2003) Science 300:100-104

OME XML File Schema:
http://www.openmicroscopy.org/docs.html
Swedlow et al (2003) Science 300:100-104

• XML File Schema:
http://www.openmicroscopy.org/docs.html
• An Updated SVG-based Image Viewer
Swedlow et al (2003) Science 300:100-104

• XML File Schema:
http://www.openmicroscopy.org/docs.html
• An Updated SVG-based Image Viewer
• Use of Semantic Typing for Data Storage & Manipulation
¸ Support for analysis steps and paths
¸ Multiple levels of attributes
¸ Extensibility of database schema
Swedlow et al (2003) Science 300:100-104

An Informatics Continuum
Live HeLa Cell
GFP-coilin
YFP-histone H2B
Platani et al (2002) Nature Cell Biol. 4:502-508

CB
WF/CCD Microscope +
10 mW solid state laser @ 488 nm
Nucleoplasm

– Encodes exactly which modules and intermediate results were used to calculate a given piece of data.
– Provides the precise description of an analysis result
– In most cases, obviates the need for an external, agreed “standard”
Swedlow et al (2003) Science 300:100-104

• Analysis modules perform small computations
• Modules linked together into analysis chains to perform larger, more useful computations
Swedlow et al (2003) Science 300:100-104

• Inputs, outputs, and links are all strongly semantically typed
• Semantic types define the way in which modules can link together
Swedlow et al (2003) Science 300:100-104

• Any directed acyclic graph (DAG) is a valid analysis chain
• Of course, a more complex graph is entirely possible
(and likely):
Swedlow et al (2003) Science 300:100-104

• New semantic types and analysis modules can be added to OME
– Both are defined by an
XML specification
– Database tables used to store metadata are derived from XML spec
– New modules can refer to existing types, allowing them to link to existing modules
Swedlow et al (2003) Science 300:100-104

OME Design and Use

Open Microscopy Environment
Jason Swedlow (Dundee)
Andrea Falconi
Jean-Marie Burel
Chris Allan
Ilya Goldberg (NIH)
Josiah Johnson
Erik Brauner (Harvard Med)
Peter Sorger (MIT)
Brian Hughes
Doug Creager