Gallery
=======

The gallery collects rendered notebooks for REVISE paper-facing application
cases. Use :doc:`case` 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 <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:

.. code-block:: text

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

If you rerun the wrappers in :doc:`case`, keep these paths or update the
notebook variables before executing the analysis cells.

Application Case Notebooks
--------------------------

.. raw:: html

   <div class="revise-card-grid">
     <a class="revise-card" href="../case/sp_SVC_case.html">
       <span class="revise-card-kicker">sp-SVC · hST</span>
       <h2>Visium HD spatial refinement</h2>
       <p>Run the high-definition tissue case and inspect the reconstructed
       sp-SVC output used by downstream spatial analyses.</p>
     </a>
     <a class="revise-card" href="../case/sc_SVC_case_T.html">
       <span class="revise-card-kicker">sc-SVC · Xenium</span>
       <h2>T cell molecular completion</h2>
       <p>Analyze reconstructed T-cell expression and spatial outputs for the
       P2CRC Xenium application workflow.</p>
     </a>
     <a class="revise-card" href="../case/sc_SVC_case_Monocyte.html">
       <span class="revise-card-kicker">sc-SVC · Xenium</span>
       <h2>Monocyte state analysis</h2>
       <p>Explore monocyte-focused sc-SVC outputs, downstream cell states, and
       spatial patterns from the paper case.</p>
     </a>
     <a class="revise-card" href="../case/sc_SVC_case_Fibroblast.html">
       <span class="revise-card-kicker">sc-SVC · Xenium</span>
       <h2>Fibroblast spatial programs</h2>
       <p>Inspect fibroblast reconstruction outputs and downstream analyses for
       pathway activity and spatial organization.</p>
     </a>
     <a class="revise-card" href="../case/sc_SVC_case_Visium_mouse_brain.html">
       <span class="revise-card-kicker">sc-SVC · Visium</span>
       <h2>Mouse brain Visium example</h2>
       <p>Open the spot-based Visium mouse cortex case that runs through the
       public REVISEPipeline API and saves notebook QC figures.</p>
     </a>
   </div>

.. toctree::
   :hidden:
   :maxdepth: 1

   sp-SVC Visium HD <../case/sp_SVC_case>
   sc-SVC T cells <../case/sc_SVC_case_T>
   sc-SVC Monocyte <../case/sc_SVC_case_Monocyte>
   sc-SVC Fibroblast <../case/sc_SVC_case_Fibroblast>
   sc-SVC Visium mouse brain <../case/sc_SVC_case_Visium_mouse_brain>