An Imaris XTension to load images and ROIs from an OMERO server directly into Imaris.
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.
- 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.
- 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)
| Dependency | Version |
|---|---|
| simple-omero-client | 5.19.0 |
| imaris-lib | 10.0.0 |
mvn clean packageThis produces a fat JAR with all dependencies:
target/omeroXT-1.0.0-SNAPSHOT-jar-with-dependencies.jar
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.jarfr.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)
This project is licensed under the GNU General Public License v2.0+.
- Pierre Pouchin — iGReD (INSERM U1103 / CNRS UMR 6293 / UCA)
- Repository: https://github.com/GReD-Clermont/omeroXT
- Issues: https://github.com/GReD-Clermont/omeroXT/issues
- Image.sc Forum: https://forum.image.sc/tag/omero