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OMEROXT

An Imaris XTension to load images and ROIs from an OMERO server directly into Imaris.

Description

omeroXT is a Java-based Imaris XTension that bridges OMERO and Imaris, enabling users to browse an OMERO server and load images and regions of interest (ROIs) into a running Imaris instance through a graphical interface.

Features

  • Connect to OMERO: Log in to an OMERO server and browse projects, datasets, and images.
  • Load images: Transfer image data (8-bit, 16-bit, and float) from OMERO to Imaris, including channel colors/names, spatial calibration, and acquisition metadata.
  • Load ROIs as Spots: Convert OMERO point ROIs into Imaris Spots objects.
  • Load ROIs as Surfaces: Convert OMERO shape ROIs (rectangles, ellipses, polygons, etc.) into Imaris Surfaces using label images.
  • Split Surfaces: Load each ROI as a separate named Surfaces object inside an Imaris data container.

Requirements

  • Java: JDK 8 or higher
  • Imaris: 10.0+ (with the ImarisLib Java library)
  • OMERO server: A running OMERO instance (>= 5.6))
  • Maven: 3.6+ (for building)

Dependencies

Dependency Version
simple-omero-client 5.19.0
imaris-lib 10.0.0

Building

mvn clean package

This produces a fat JAR with all dependencies:

target/omeroXT-1.0.0-SNAPSHOT-jar-with-dependencies.jar

Usage

Standalone

When starting the application from the JAR file, it will detect running Imaris instances and let you select one from the GUI:

java -jar omeroXT-1.0.0-SNAPSHOT-jar-with-dependencies.jar

Project Structure

fr.igred
├── imaris
│   ├── gui         — GUI components (main window, connection dialog)
│   ├── omero       — Service layer bridging OMERO and Imaris
│   └── xtension    — Main entry point (OMEROXTension)
└── omero
    ├── repository   — Image-to-Imaris conversion (Image2Imaris)
    └── roi          — ROI-to-Imaris conversion (ROI2Imaris)

License

This project is licensed under the GNU General Public License v2.0+.

Authors

  • Pierre Pouchin — iGReD (INSERM U1103 / CNRS UMR 6293 / UCA)

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