Add Fluorescence Images to Seurat object

[leejs0620]

Hi, Thank you for the great working on the Seurat package.

I ran SpaceRanger for my samples and loaded them by the function "Load10X_Spatial". The Seurat object includes an image down-sampled(low-resolution) by SpaceRanger. Even though I input four fluorescence Images for the same sample in running SpaceRanger, the output includes only one image. So I want to add more fluorescence Images in the Seurat object for further analysis. I know that there is a function named "Read10X_Image()". It requires an image down-scaled by SpaceRanger pipeline. But I have only original images that have huge pixels. I think that adding the original images in the Seurat object is very inefficient and 10X does not open the exact way for image processing algorithm. Could you please consider the new function for down-scaling the image and adding the images in Seurart object??

[dcollins15]

Do you know the mapping between the coordinates in the tissue_positions.csv file and the images you'd like to add?

For the images given by SpaceRanger the scalefactors_json.json file typically contains this information. If you knew the mapping you could generate your own set of scale factors to handle the coordinate mapping.

Unfortunately, a function like the one you described is well out of the scope of Seurat.