Check Image Alignment

The tracklines on the chip surface act as markers to help with image registration. They are created when the capturing probe is unloaded and will show up as narrow lines on the spatial feature expression density heatmap. A good alignment is achieved when the tracklines perfectly overlap with the lines visible on the image. Highly recommend zooming in on the tissue edges to check the quality of the alignment.

A small tip for examining alignment, begin by inspecting the two diagonal fields of view. If these views perfectly overlap, it’s likely that the overall alignment is suitable.

However, if most of the track lines do not overlap, you will need to realign the image manually. Refer to the Navigation for Image Processing for instructions on how to do this.

If the tracklines overlap perfectly in one field of view but are mismatched in the diagonal view, it could indicate an issue due to stitching problems in your microscope image.