Gallery

The gallery collects rendered notebooks for REVISE paper-facing application cases. Use Application Mode for the command-line routes that generate application outputs, then use the notebooks below to inspect downstream biological analyses and figures.

Prepare Data

Before opening the application case notebooks, download the REVISE data archive from Zenodo:

https://zenodo.org/record/17607778

The archive contains the Sim2Real-ST benchmark data, intermediate results, and final predictions generated for REVISE. Download Result.zip from the Zenodo record and extract it at the repository root so the notebook paths resolve to the expected local folders, including raw_data/ and generated output directories.

For application case notebooks, the relevant inputs are the real application data and the notebook-compatible outputs produced by the application wrappers:

raw_data/Real_application/
output/sp_SVC_case/
output/sc_SVC_case/

If you rerun the wrappers in Application Mode, keep these paths or update the notebook variables before executing the analysis cells.

Application Case Notebooks

sp-SVC · hST

Visium HD spatial refinement

Run the high-definition tissue case and inspect the reconstructed sp-SVC output used by downstream spatial analyses.

sc-SVC · Xenium

T cell molecular completion

Analyze reconstructed T-cell expression and spatial outputs for the P2CRC Xenium application workflow.

sc-SVC · Xenium

Monocyte state analysis

Explore monocyte-focused sc-SVC outputs, downstream cell states, and spatial patterns from the paper case.

sc-SVC · Xenium

Fibroblast spatial programs

Inspect fibroblast reconstruction outputs and downstream analyses for pathway activity and spatial organization.

sc-SVC · Visium

Mouse brain Visium example

Open the spot-based Visium mouse cortex case that runs through the public REVISEPipeline API and saves notebook QC figures.