The Open Microscopy Environment: A Collaborative Data Modeling and Software Development Project for Biological Image Informatics

  • Jason R. Swedlow
Part of the Principles and Practice book series (PRINCIPLES)

The transition of a microscope’s output from an “image,” recorded on paper or film, to digitally recorded “data” has created new demands for storage, analysis and visualization that are not adequately met in current software packages. The Open Microscopy Environment (OME) Consortium is dedicated to developing open available tools to meet this challenge. We have developed and released the OME data model that provides a thorough description of the image data acquisition, structure and analysis results. An XML representation of the OME data model provides convenient standardized file formats known as OME-XML and OME-TIFF. In addition, OME has built two software tools, the OME and OME Remote Objects (OMERO) servers that enable visualization, management and analysis of multidimensional image data in structures that enable remote access. The OME server provides a flexible data model and an interface into complex analysis workflows. The OMERO server and clients provide image data visualization and management. A major goal for the next year is the provision of well-developed libraries and documentation to support the OME file formats, and enhanced functionality in our OME and OMERO applications to provide complete solutions for imaging in cell biology.


File Format Optical Computation Analysis Engine Image Informatics Image Data Acquisition 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Andrews PD, Harper IS, Swedlow JR (2002) To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era. Traffic 3:29–36.CrossRefPubMedGoogle Scholar
  2. Castleman KR (1979) Digital image processing. Prentice Hall, Englewood Cliffs.Google Scholar
  3. Conrad C, Erfle H, Warnat P, Daigle N, Lorch T, Ellenberg J, Pepperkok R, Eils R (2004) Automatic identification of subcellular phenotypes on human cell arrays. Genome Res 14:1130–1136.CrossRefPubMedGoogle Scholar
  4. Eils R, Athale C (2003) Computational imaging in cell biology. J Cell Biol 161:477–481.CrossRefPubMedGoogle Scholar
  5. Free Software Foundation (2007a) GNU general public license. Cited 19 April 2007.
  6. Free Software Foundation (2007b) GNU lesser general public license. Cited 19 April 2007.
  7. Giepmans BN, Adams SR, Ellisman MH, Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312:217–224.CrossRefPubMedGoogle Scholar
  8. Goldberg IG, Allan C, Burel J-M, D. Creager D, Falconi A, Hochheiser HS, Johnston J, Mellen J, Sorger PK, Swedlow JR (2005) The Open Microscopy Environment (OME) data model and XML File: open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6:R47.Google Scholar
  9. Hibernate (2007) Red Hat Middleware, Rayleigh. Cited 19 April 2007.
  10. ImageJ (2007) ImageJ. Cited 19 April 2007.
  11. (2007) JBoss, Atlanta. Cited 19 April 2007.
  12. Kiger A, Baum B, Jones S, Jones M, Coulson A, Echeverri C, Perrimon N (2003) A functional genomic analysis of cell morphology using RNA interference. J Biol 2:27.CrossRefPubMedGoogle Scholar
  13. Laboratory for Optical Computation and Instrumentation (2007a) LOCI. Cited 19 April 2007.
  14. Laboratory for Optical Computation and Instrumentation (2007b) OME at LOCI–OME-TIFF–OME-TIFF specification. Cited 19 April 2007.
  15. Laboratory for Optical Computation and Instrumentation (2007c) OME at LOCI–software–Bio-Formats library. Cited 19 April 2007.
  16. Lippincott-Schwartz J, Snapp JE, Kenworthy A (2001) Studying protein dynamics in living cells. Nat Rev Mol Cell Biol 2:444–456.CrossRefPubMedGoogle Scholar
  17. (2007) MySQL, Uppsala. Cited 19 April 2007.
  18. Open Microscopy Environment (2007a) About OME. Cited 19 April 2007.
  19. Open Microscopy Environment (2007b) OME examples. Cited 19 April 2007.
  20. Open Microscopy Environment (2007c) Schema doc. Cited 19 April 2007.
  21. Open Microscopy Environment (2007d) OME-XML evolution. Cited 19 April 2007.
  22. Open Microscopy Environment (2007e) Analysis chains. Cited 19 April 2007.
  23. Open Microscopy Environment (2007f) Image analysis with MATLAB. Cited 19 April 2007.
  24. Open Microscopy Environment (2007g) Introduction to OME-XML schemas. Cited 19 April 2007.
  25. Open Microscopy Environment (2007h) OME Web client “Marino”. Cited 19 April 2007.
  26. Open Microscopy Environment (2007i) Source directory of /OME/src/Excel. Cited 19 April 2007.
  27. Open Microscopy Environment (2007j) 19 April 2007.
  28. Open Microscopy Environment (2007k) OME-downloads. 19 April 2007.
  29. Open Microscopy Environment (2007l) OMERO Trac. 19 April 2007.
  30. Open Microscopy Environment (2007m) Introduction to the OME-XML schema. Cited 19 April 2007.
  31. Oracle (2007) Oracle 10g. Cited 19 April 2007.
  32. Phair RD, Misteli T (2001) Kinetic modelling approaches to in vivo imaging. Nat Rev Mol Cell Biol 2:898–907.CrossRefPubMedGoogle Scholar
  33. Platani M, Goldberg I, Lamond AI, Swedlow JR (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502–508.CrossRefPubMedGoogle Scholar
  34. PostgreSQL (2007) PostgreSQL Global Development Group. Cited 19 April 2007.
  35. Schiffmann DA, Dikovskaya D, Appleton PL, Newton IP, Creager DA, Allan C, Nathke IS, Goldberg IG (2006) Open microscopy environment and FindSpots: integrating image informatics with quantitative multidimensional image analysis. BioTechniques 41:199–208.CrossRefPubMedGoogle Scholar
  36. Schiffman DA, Appleton PL, Goldberg IG (2007) FindSpots (OME v2.5.1) user guide. Available at Cited 19 April 2007.
  37. Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S (2000) Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 1:287–292.CrossRefPubMedGoogle Scholar
  38. Sun Microsystems (2007) Remote method invocation home. Cited 19 April 2007.
  39. Swedlow JR, Goldberg I (2006) Data models across labs, genomes, space, and time. Nat Cell Biol 8:1190–1194.CrossRefPubMedGoogle Scholar
  40. Swedlow JR, Sedat JW, Agard DA (1997) Deconvolution in optical microscopy. In: Jansson PA (ed) Deconvolution of images and spectra. Academic, New York, pp 284–309.Google Scholar
  41. Swedlow JR, Goldberg I, Brauner E, Sorger PK (2003) Informatics and quantitative analysis in biological imaging. Science 300:100–102.CrossRefPubMedGoogle Scholar
  42. The R Project (2007) The R project for statistical computing. Cited 19 April 2007.
  43. The Usable Image Project (2007) The usable image project. Cited 19 April 2007.
  44. Wouters FS, Verveer PJ, Bastiaens PI (2001) Imaging biochemistry inside cells. Trends Cell Biol 11:203–211.CrossRefPubMedGoogle Scholar
  45. Yarrow JC, Feng Y, Perlman ZE, Kirchhausen T, Mitchison TJ (2003) Phenotypic screening of small molecule libraries by high throughput cell imaging. Comb Chem High Throughput Screen 6:279–286.PubMedGoogle Scholar
  46. ZeroC (2007) Welcome to ZeroC, the home of Ice. Cited 19 April 2007.
  47. (2007) Cited 19 April 2007.

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Jason R. Swedlow
    • 1
  1. 1.Division of Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUK

Personalised recommendations