Question: How can I verify the fiducial frame alignment for Visium HD was successful?
Answer: To verify if the fiducial frame alignment was successful, open the web summary HTML file and navigate to the “Image Alignment” tab. Then, check the “Tissue Detection and Fiducial Alignment” image. If the red circles do not uniformly encircle the fiducials in the fiducial frame, the alignment has failed. While this may be noticeable without zooming in, it is recommended to zoom in on the fiducials to check for subtle misalignments, as shown below.
Visium HD CytAssist image with a subtle fiducial frame misalignment
Visium HD CytAssist image with the correct fiducial frame alignment
If the CytAssist Image was generated from a CytAssist instrument using firmware version 2.1, please see "How do I correct the red channel shift observed in my CytAssist image when running instrument firmware version 2.1?" for additional guidance.
If you would like guidance on how to check the instrument firmware version please see “How do I find the CytAssist instrument firmware version that generated my CytAssist image?”
In all other cases, to correct the fiducial frame alignment, perform a manual alignment using Loupe Browser. For more details, please visit our support site at the following link.
Last Updated: Oct. 2024