Tutorials
============
This section consists of various cases which will make you familiar with the process of 
main analysis. If you want to dig deeper, **API** could give more information.


.. card:: Basic Workflow
    :octicon:`book;1em;`
    :link: Basic_Workflow
    :link-type: doc

    This section contains main preprocessing and analysis on single-cell data, including Square Bin and Cell Bin cases.

.. card:: Data Preprocessing
    :octicon:`book;1em;`
    :link: Data_Preprocessing
    :link-type: doc

    This section contains main preprocessing and analysis on single-cell data, including Square Bin and Cell Bin cases.

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

    This section introduces methods to annotate cells automatically, according to given reference.


.. card:: Cell Analysis
    :octicon:`book;1em;`
    :link: Cell_Analysis
    :link-type: doc

    This section introduces how to perform functions on cell level.


.. card:: Gene Analysis
    :octicon:`book;1em;`
    :link: Gene_Analysis
    :link-type: doc

    This section introduces how to perform functions on gene level.


.. card:: Cell Fate Inference
    :octicon:`book;1em;`
    :link: Cell_Fate_Inference
    :link-type: doc

    This section introduces several functions to infer the cell fate.


.. card:: Image Processing
    :octicon:`book;1em;`
    :link: Image_Processing
    :link-type: doc

    This section contains various examples from the :mod:`stereo.im` and :mod:`stereo.tools` module.


.. card:: Interactive Visualization
    :octicon:`book;1em;`
    :link: Interactive_Visualization
    :link-type: doc

    This section shows how to perform interactive plotting and export the region of interest.


.. card:: Performance Optimization
    :octicon:`book;1em;`
    :link: Performance_Optimization
    :link-type: doc

    This section shows how to accelerate functions and the test results of performance.



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

    Basic_Workflow
    Data_Preprocessing
    Annotation
    Cell_Analysis
    Gene_Analysis
    Cell_Fate_Inference
    Image_Processing
    Interactive_Visualization
    Performance_Optimization