API Reference
=============

This section provides detailed API documentation for all Phenotypic modules and functions.

Image
-----

.. currentmodule:: phenotypic

.. toctree::
   :maxdepth: 2

   core/image_methods
   core/color_space_operations
   core/visualization_plotting

GridImage
---------

.. toctree::
   :maxdepth: 2

   core/grid_image_methods


ImagePipeline
-------------

.. toctree::
   :maxdepth: 2

   core/image_pipeline_methods

GUI internals
-------------

.. toctree::
   :maxdepth: 1

   gui/index

Reference Pages
---------------

.. toctree::
   :maxdepth: 1

   cli_reference
   config_reference
   glossary

Modules
-------
.. currentmodule:: phenotypic
.. autosummary::
   :toctree: api/
   :caption: Modules
   :template: module.rst
   :recursive:

   phenotypic
   phenotypic.abc_
   phenotypic.analysis
   phenotypic.correction
   phenotypic.data
   phenotypic.detect
   phenotypic.enhance
   phenotypic.grid
   phenotypic.measure
   phenotypic.prefab
   phenotypic.refine
   phenotypic.sdk_
   phenotypic.tune
   phenotypic.util