.. Spider documentation master file, created by
   sphinx-quickstart on Sat Jul 12 01:03:20 2025.
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Welcome to Spider's documentation!
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Spider – a flexible and unified framework for simulating ST data.
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.. toctree::
   :maxdepth: 1 
   :caption: Contents:

   Installation
   Reference-based_simulation
   Benchmark_datasets_generation
   TIME_simulation
   3D_simulation

.. image:: ../figures/workflow.png
   :width: 1400

Overview
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Spider is a flexible and unified framework for simulating ST data by leveraging spatial neighborhood patterns among cells through a conditional optimization algorithm. 
By inputting spatial patterns extracted from real data or user-specified transition matrix, 
Spider assigns cell type labels through the BSA algorithm that improves the computational efficiency of conventional simulated annealing algorithm. 
Gene expression profiles for individual cell types can be generated either using real or simulated data by Splatter or scDesign2. 
Finally, spot-level ST data can be simulated by aggregating cells inside generated spots using 10X spatial encoding scheme or user-specified generation rules.