ORION Whole Slide Multiplexed Imaging
ORION is a method for collecting one-shot and multi-cycle 18-plex immunofluorescence images and diagnostic-grade H&E images from the same samples. The Orion method was developed in collaboration with RareCyte Inc. and uses a specialized microscope and fluorescent antibodies, which can be imaged simultaneously and spectrally unmixed. Same-slide H&E and IF images provide complementary information that can be used to train ML models to predict cancer progression.
For the Breast Atlas, ORION is performed to visualize distinct markers and quantify the expression and spatial heterogeneity of markers across ROIs corresponding to normal breast and benign regions.
About the Data
Method and Protocol
Learn about the Orion method by reading:
- Lin, JR., Chen, YA., Campton, D. et al. Nature Cancer (2023). DOI: 10.1038/s43018-023-00576-1
Data Visualization
Full-resolution images can be viewed in a web browser using Minerva:
- via the gallery (forthcoming)
- in cBioPortal (forthcoming)
Learn more about the Minerva software at minerva.im.
Data Access
All image data will be accessible from Amazon Web Services (AWS):
- Levels 1-2: OME-TIFF
- Level 3: OME-TIFF
- Level 4: csv
For a description of the files see the table below.
About the Samples
The following are planned to image with Orion:
- 50-100 normal breast samples
- 75 ovarian samples
Instruments
Orion data was collected on RareCyte Orion 6 and 11 microscopes.
About the Data Generators
This data was generated and analyzed by the Laboratory of Systems Pharmacology at Harvard Medical School.
Data Levels:
Orion uses OME-TIFF and other BioFormats file formats and follows MITI standards.
| Data Type | Description | File Format | Average size (per sample) | Data Location |
|---|---|---|---|---|
| High-plex image data (Levels 1-2) | Quality controlled images are assembled into a high-plex whole slide image | OME-TIFF | 100 GB | AWS |
| Segmentation masks (Level 3) | Cell segmentation identifies and separates cell, nucleus, cytoplasm and other regions | OME-TIFF | 0.5 GB | AWS |
| Single-cell spatial feature tables (Level 4) | Summarize the expression of marker intensities and morphological features for each cell | csv | 1 GB | AWS |