I assumed from the single cell analysis Fig 4 in the Cell paper that it is possible to match exactly the transcriptomic barcode coordinates with the pixel coordinates of the H&E image.
Perhaps I am missing something, but I cannot see any command line argument that would allow inclusion of the H&E images in the analysis, nor can I see any H&E images embedded in the resulting RDS files, including file Liver_normal_Segmentation_Hepatocytes.rds from the companion web page, https://doi.org/10.7302/cjfe-wa35.
How were transcriptome barcode spatial coordinates and H&E image pixel coordinates matched?
First of all thanks for sharing your code.
I assumed from the single cell analysis Fig 4 in the Cell paper that it is possible to match exactly the transcriptomic barcode coordinates with the pixel coordinates of the H&E image.
Perhaps I am missing something, but I cannot see any command line argument that would allow inclusion of the H&E images in the analysis, nor can I see any H&E images embedded in the resulting RDS files, including file
Liver_normal_Segmentation_Hepatocytes.rdsfrom the companion web page, https://doi.org/10.7302/cjfe-wa35.How were transcriptome barcode spatial coordinates and H&E image pixel coordinates matched?