Can Spotiphy be used with Stereo-seq data (ssDNA-stained images)?

[wuliRothschild]

Hi, Spotiphy authors!
This method looks very interesting. I’m currently analyzing a Stereo-seq sample that lacks paired HE-stained images but instead uses ssDNA-stained images for nuclei localization and segmentation. In this case, how can I proceed with using Spotiphy for analysis?
Thank you very much!

[ZiqianZheng]

Hi wuliRothschild,

Thank you for using our tool!

To use Spotiphy with Stereo-seq samples that lack paired HE-stained images, you will need to implement custom code to perform the following steps:
– Load the Stereo-seq data as an AnnData object.
– Estimate the number of cells at each spatial location using the ssDNA-stained image.

We’re actively developing functions and tutorials for Stereo-seq analysis and will let you know as soon as they’re released!

Best,
Ziqian Zheng