Question: Can I align my H&E image and IF stained images to each other using Loupe Browser for my Visium data?
Answer: Loupe Browser is a visualization tool by 10x Genomics which has alignment functionality for manual alignment of CytAssist images (bright field image) with high resolution microscope images (H&E or IF) and/or fiducial alignment to identify the fiducial markers in the Visium slide. Any other use cases besides the ones discussed are not officially supported.
The following analysis guide article discusses the image registration in the context of Xenium DAPI images with an H&E image but the same steps could be followed with a fluorescence stained image of the same sample from a Visium assay as well.
H&E to Xenium DAPI Image Registration with Fiji
Note: 10x Genomics does not provide support for community-developed tools and makes no guarantees regarding their function or performance. Please contact tool developers with any questions.
Products: Visium Spatial Gene Expression for FFPE, Visium Spatial Gene Expression for FF, Visium CytAssist Gene Expression, Visium CytAssist Gene and Protein Expression