Optical Target Test

Before processing images for the Illumina Spatial Transcriptome Assay, the Optical Target Test should be performed using the Illumina Bright Field (BF) Optical Target. This test is intended to evaluate whether the image quality produced by a microscope is suitable for use with the Illumina Spatial Transcriptome Assay. The images captured during this test are used as input for the Illumina Spatial Image Tool (ISIT) during the Assess Microscope workflow.

The Optical Target Test is designed for use with microscopes and is not intended for slide scanner imaging systems.

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.

The Optical Target Test provides the following key metrics:

• Estimated pixel size (microns) of the camera
• Full Width Half Maximum (FWHM) for assessing focus quality
• Shading uniformity observed in the FOV
• An optical distortion heatmap

The Illumina BF Optical Target is a 75 mm x 25 mm x 1 mm slide featuring patterned elements in the center. This test must be conducted using the 20X objective lens and the specific camera intended to be used with the Illumina Spatial Transcriptome Assay. The microscope assessment includes evaluation of focus quality, detection of stage tilt, analysis of optical distortion, and assessment of shading uniformity. These metrics are valuable for diagnosing and troubleshooting image quality issues.

Here are the articles in this section:

• Imaging the Illumina Optical Target
• Microscope Assessment