Tutorials

This section provides end-to-end DeepSpatial tutorials across multiple spatial omics datasets. Each tutorial follows a consistent workflow:

1. Import dependencies.

2. Prepare slice-level data.

3. Set up and train DeepSpatial.

4. Reconstruct a full 3D volume.

5. Visualize and inspect results.

Tutorial Catalog

• Mouse Hypothalamus MERFISH: Reconstruction from serial MERFISH slices with physical inter-slice spacing.

• Human Breast Cancer IMC: Reconstruction from IMC slices using 3D coordinates split into XY (spatial) and Z (z_coord).

• Mouse Brain DeepStarMap: 3D validation workflow for evaluating reconstructed mouse brain structures.

• Mouse Hypothalamus MERFISH 3D Reconstruction
• Human Breast Cancer IMC 3D Reconstruction
• Mouse Brain Deep STARmap 3D Validation