Tutorials
============
This section consists of various cases which will make you familiar with the process of main analyses.

.. card:: WACCA
    :octicon:`book;1em;`
    :link: Preprocess
    :link-type: doc

    This section contains a Whole-Animal reconstruction pipeline using 2D multimodal registration, Cell segmentation, Clustering, and Annotation to integrate the series of Stereo-seq slices and obtain comprehensive 3D anatomic and molecular profiles.

.. card:: SPC analysis
    :octicon:`book;1em;`
    :link: BIO
    :link-type: doc

    This section contains a pipeline for spatial proximity-based clustering (SPC) to group similar cells into the same cluster based on both transcriptional similarity and spatial proximity, as well as downstream analyses.

.. card:: Polarity analysis
    :octicon:`book;1em;`
    :link: PCG
    :link-type: doc

    This section contains main analyses on polarity-related genes to capture positional gradients along the body axis.

.. card:: Other modules
    :octicon:`book;1em;`
    :link: Other
    :link-type: doc

    This section introduces various methods to meet user-defined requirements, such as body straightening and blastema detection.

.. toctree::
    :titlesonly:
    :maxdepth: 1
    :hidden:
    
    Preprocess
    BIO
    PCG
    Other