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

.. toctree::
   :caption: Tutorials
   :maxdepth: 1

   notebooks/Tutorial_1_VisiumHD_ROI_selection_colon.ipynb
   notebooks/Tutorial_2_CosMx_FOV_selection_kidney.ipynb
   notebooks/Tutorial_3_Consecutive_ROI_selection_breast.ipynb
   notebooks/Tutorial_4_TMA_selection_breast.ipynb