10x Genomics Support/Space Ranger/Analysis/

Manual Alignment for Visium

In most cases, Space Ranger will automatically align microscope images with CytAssist images and expression data captured on the Visium slide. If manual alignment is necessary, choose the option that best fits your experiment.

Visium HD Manual Alignment

Identify fiducials, perform tissue selection and align CytAssist and microscope images for Visium HD. You will then export a JSON file for Space Ranger analysis.

Manual Fiducial Alignment and Tissue Detection

Manually identify the fiducials in your Visium image and select spots under tissue. You will then export a JSON file for Space Ranger analysis.

Manual CytAssist Image - Microscope Image Alignment

Align your CytAssist image and microscope image. After you complete this step, you can either export a JSON file for Space Ranger automated fiducial and tissue detection, or continue to Visium Fiducial Alignment.