Integration of OMERO with ICY


Balaji Ramalingam


  • Introduction to ICY
    • ICY and Bio-Formats
    • ICY Image Structure
    • ICY and ImageJ
    • ICY Plugins and Blocks
  • Intregration Status
    • OMERO and ICY Prototypes
    • Current Issues and Future Plans

ICY and Bio-Formats

  • No Installation Required

ICY Image Structure

  • A Sequence is basically a 5 dimension (XYCZT) image where :
    • XY dimension = planar image ; C dimension = channel
    • Z dimension = depth ; T dimension = time

    The XYC dimensions are bounded into the IcyBufferedImage object so Sequence define a list of IcyBufferedImage where each image is associated to a Z and T information.

ICY and ImageJ

  • Native ImageJ Integration

ICY Plugins and Blocks

OMERO and ICY Prototypes

  • OMERO Login and Import Image
  • OMERO Export
  • OMERO Data Tree (In Progress)


  • Current Issues
    • ICY uses Bio-Formats 5.0.8 and the upgrade is not straight-forward
    • Running the OMERO-IJ Plugin under ICY-ImageJ did not work!!!
    • ICY Blocks are not meant to be used with Event-listeners
    • OMERO To ICY Prototype : depends on BioFormats Importer(via ImageJ)-Not Ideal for big images
  • Future Plans
    • ICY omero Importer independent of ImageJ?
    • Move the prototypes to the OMERO code base and use the Gateway classes?
    • Send ROI's back to OMERO
    • Send Results Table back to OMERO

Thank you