Align images (e.g. H&E)
If you have an H&E image or immunofluorescence data that you want to align on the main image, this can be done with the Xenium Explorer, even if you don't work on Xenium data.
Image conversion
Convert your image with QuPath as written in this 10x genomics webpage.
If you are not familiar with QuPath, you can also use our API to write the image:
import sopa.io
image = sopa.io.ome_tif("path/to/your/image.tif") # or use a different reader
sopa.io.write_image("where/to/save/image.ome.tif", image, is_dir=False)
Xenium users
If using the Xenium machine, then you don't need conversion; the images provided by the Xenium machine already have the correct format.
Open your data in the Xenium Explorer
If not done yet, convert your SpatialData object to the Xenium Explorer's inputs. This can be done as detailed in this tutorial.
Double-click on the experiment.xenium file, or select it from the Xenium Explorer interface. It will display the data in the explorer.
Keypoint placement
Warning
Make sure your Xenium Explorer version is at least 1.3.0
On the Xenium Explorer, under the "Images" panel, click "Add image" and follow the instructions on the screen.
Afterwards, the explorer will automatically align the images based on the key points you selected on both images.
(Optional) Update the SpatialData object
After alignment, export the transformation matrix as a .csv file. For that, select your aligned image under the "Images" panel and click on "Download Alignment File":
Then, select only the "Transformation Matrix" box and download it:
Then, use the CLI to update your SpatialData object. You'll need the path to the .zarr directory corresponding to your SpatialData object (SDATA_PATH), the path to the .ome.tif image that you converted above (IMAGE_PATH), and the .csv transformation matrix that you exported from the Xenium Explorer (TRANSFORMATION_MATRIX_PATH):