Tutorials

Here are the tutorials for the demo datasets .

To run the tutorials, first please download the demo data and pretrained model checkpoints file from:

google drive: https://drive.google.com/drive/folders/1z1nk0sF_e25LKMyHxJVMtROFjuWet2G_?usp=sharing

Please place both ‘checkpoints’ and ‘demo’ folder under the ‘S2Omics’ main folder.

We offer four tutorials handling diverse cases:

  • Tutorial 1 is about designing VisiumHD experiment on a colorectal cancer section, including ROI selection and cell type label broadcasting

  • Tutorial 2 is about designing CosMx experiment on two kidney sections (a healthy one and a T2D one), including both ROI and FOV selection

  • Tutorial 3 is about designing spatial omics experiment on three consecutive breast cancer sections, including ROI selection

  • Tutorial 4 is about designing TMA experiment on a slide containing multiple breast cancer biopsyes, this tutorial includes circle-shaped ROI selection

Tutorials