The Open Microscopy Environment:
Informatics & Quantitative Analysis for
Biological Microscopy, HCAs & Image Repositories
Jason Swedlow
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
University of Dundee
Scotland
Glencoe Software, Inc
Seattle, WA
USA
The Image Problem
• A pretty picture?
• A measurement?
The Image Problem
• A pretty picture?
• A measurement?
Organelles
Cells
Lead Discovery
Target Validation
Physiology
Dynamics
Pathology
In Vivo
Current Imaging Workflow Paradigm
No Standards
Experiment?
Treatment?
Image?
Analytics?
Annotations?
Maybe it’s not boring…
Maybe it’s not boring…
What is complex data (for us)?
•  Our focus is local– what happens in single lab
•  Experiment-driven data acquisition
  output is a “result”, not shared data
  most data is garbage
•  Data generation is from (multiple) proprietary platforms
•  A modern biomedical lab is an enterprise data generator:
8 data collectors, 2 – 20 different acquisition platforms,
10 – 1000 samples per acquisition, 0.1 – 20 GB/sample
•  Heterogeneous training in data processing, curation,
& retention
•  Experimental applications & models evolve on the timescale
of months (at least); so must all useful informatics tools
•  Tools that enable discovery are used, regardless of pain
and misery involved. Tools that don’t are discarded.
Complex Data: Mitotic spindle orientation in
neurogenesis
Wilcock et al, 2007.
Wilcock et al (2007)
55 4D images; ~5 GB each
Max intensity projection. 30 sections @ 1.5µm; 7min timelapse,
38 hours
Complex Data: Mitotic Kinetochore Dynamics
GFP-CENP-A HeLa Stable Cell Line
MBL Kinetochore Consortium
Danuser, McAinsh, Meraldi, Swedlow Labs
Fully validated cell handling & perturbation
Defined imaging protocol
Correct temporal sampling (7.5s/3D stack)
Wilcock et al, 2007.
Fully automated processing pipeline
Jaqaman et al (2010)
Complex Data: Mitotic Kinetochore Dynamics
Condition
Control
Control (synchronised)
Nocodazole
Taxol
Fixed
Hec1 siRNA
Nuf2 siRNA
MCAK siRNA
WilcockKIF18A
et al, siRNA
2007.
Cenp-E siRNA
Cenp-E siRNA + taxol
CAPD2 siRNA
Separase siRNA
Bub1 siRNA
Mad1 siRNA
Mad2 siRNA
BubR1 siRNA
MG132
Total
`
Number of cells
293
36
34
19
10
17
18
71
24
68
72
33
41
31
47
16
10
36
876
Aligned sister pairs
11962
1293
1259
520
400
584
587
3281
631
1951
2345
710
1466
1161
1532
301
244
1194
31421
Current Imaging Workflow Paradigm
No Standards
Experiment?
Treatment?
Image?
Analytics?
Annotations?
Towards Image Informatics
Reqs for Image Informatics?
Interoperability
 Metadata
 Interfaces
OME: Brief Overview
• Founded 2000 by J. Swedlow, P. Sorger, I. Goldberg
• Funded by Wellcome Trust, BBSRC, EPSRC, NIH
• Partnered with other image informatics efforts (LOCI,
UCSB, VU, NCBO, EPCC, EBI…) and many commercial
imaging companies
• Currently, Dundee, LOCI and Baltimore are main
development sites
• Open source (LGPL & GPL), nightly release
• Initial goal: provide image informatics infrastructure for
biological microscopy
OME: Brief Overview
• Founded 2000 by J. Swedlow, P. Sorger, I. Goldberg
• Funded by Wellcome Trust, NIH, BBSRC, EPSRC
• Partnered with other image informatics efforts (LOCI,
UCSB, VU, NCBO, EPCC, EBI…) and many commercial
imaging companies
• Currently, Dundee, LOCI and Baltimore are main
development sites
• Open source (LGPL & GPL), nightly release
• Current goal: Development and integration of usable,
effective tools for image data management,
visualization and analysis
OME: What We Do
OME Data Model
Open,
Exchangeable
file formats
Open Image Data
Management
Software
The OME Data Model: http://www.ome-xml.org
OME: What We Do
OME Data Model
Open,
Exchangeable
file formats
OME-XML
OME-TIFF
Bio-Formats
Open Image Data
Management
Software
OME Bio-Formats:
Proprietary File Conversion
OME Bio-Formats:
Proprietary File Conversion
OME: What We Do
OME Data Model
Open,
Exchangeable
file formats
Open Image Data
Management
Software
(See movies at
http://openmicroscopy.org/videos/)
The OMERO Platform
OMERO: Tools & Workflow
OMERO.insight: Data Viz and Analysis
OMERO.insight: Data Viz, Manage & Analyze
OMERO ScreenPlateWell: High Content Assays
OMERO ScreenPlateWell: High Content Assays
OMERO.tables: HCS Analysis Results
Defining, Storage & Interfaces for ROIs
GroEL data and box-files from http://ami.scripps.edu/experiment/index.php
The OMERO Platform
ImageJ Integration with OMERO
Matlab as an OMERO Client
Calling OMERO.Blitz API from Matlab:
•  All calls go through a Java API called blitzGateway
•  Matlab wrappers for the calls
•  Allows access to most API calls and provides helper
methods for the most common operations.
Matlab as an OMERO Client
Cellprofiler Integration with OMERO
Cellprofiler Integration with OMERO
OMERO data
Cellprofiler output
in OMERO
OMERO Tools: Simple Resources for Workflow
OMERO Tools: Simple Resources for Workflow
OMERO ScreenPlateWell: Help from Outside
OME in Use
STARTS PER IP ADDRESS
================================================================
APPLICATION
EDITOR BIO-FORMATS IMPORTER INSIGHT SERVER
WEB UNIQUE IPs
292
12007
1157
1825
1398
398 OME: Warts & All
•  Funded through 2011
•  Committed to delivery & open development
•  If users reject it, we reject it too.
•  Technically, very ambitious (c.f. “data deduplication”)
•  Very collaborative, especially with groups committed to
production
Towards Image Repositories
JCB DataViewer:
Access to Original Image Data
JCB DataViewer:
Access to Original Image Data
http://openmicroscopy.org
OME: Current Team
• Dundee (Swedlow Lab) - Chris Allan, Jean-Marie Burel,
Brian Loranger, Donald MacDonald, Will Moore,
Andrew Patterson, Aleksandra Tarkowska
• Dundee (Usable Image) - Catriona Macaulay, David Sloan,
Paula Forbes, Xinyi Jiang, Scott Loynton
• Univ Wisconsin, Madison (LOCI) - Kevin Eliceiri,
Curtis Rueden
• Baltimore - Ilya Goldberg, Josiah Johnston, Tomasz Macura
• Glencoe Software - Josh Moore, Melissa Linkert, Carlos Neves
Potential conflict: JRS is a Co-Founder of Glencoe Software