Imaging Assessment

Use the Imaging Assessment to evaluate slide scanners and microscopes for the Illumina StrataMap Assay. The test confirms that fiducial markers are imaged accurately for registration and downstream analysis.

Perform the Imaging Assessment with the same 20X objective lens used for the assay. Analyze the captured images in Illumina StrataMap Image Tool (ISIT) and assess them against the image quality metrics.

The Imaging Assessment uses the same Image Processing workflow as a functional assay slide. After completing the workflow, export the images to Core and use the Illumina StrataMap Cell Segmentation Tool to review the cell segmentation results.

The StrataMap Imaging Assessment Slide provided for the Imaging Assessment may not have a slide ID. A slide ID is not required for the Imaging Assessment, so enter another identifier, such as 1234.

Illumina recommends using a slide scanner for imaging, as microscopes require manual adjustments, more experience with imaging principles, and additional training and practice for accurate results.

For detailed instructions on preparing and imaging the fiducial target slide, refer to the Illumina StrataMap Spatial Transcriptome Assay Product Documentation.