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

Function documentation is generated from in-code docstrings.

File Utilities
==============

Argument Parsing
----------------

.. automodule:: image_analysis_3D.file_utils.arg_parsing_utils
   :members:

File Checking
-------------

.. automodule:: image_analysis_3D.file_utils.file_checking
   :members:

File Reading
------------

.. automodule:: image_analysis_3D.file_utils.file_reading
   :members:

Notebook Initialization
-----------------------

.. automodule:: image_analysis_3D.file_utils.notebook_init_utils
   :members:

Preprocessing Functions
-----------------------

.. automodule:: image_analysis_3D.file_utils.preprocessing_funcs
   :members:

Channel Mapping
---------------

.. automodule:: image_analysis_3D.file_utils.read_in_channel_mapping
   :members:

Segmentation Decoupling (File Utilities)
-----------------------------------------

.. automodule:: image_analysis_3D.file_utils.segmentation_decoupling
   :members:

Errors
------

.. automodule:: image_analysis_3D.errors.exceptions
   :members:

Segmentation Utilities
======================

General Segmentation
--------------------

.. automodule:: image_analysis_3D.segmentation_utils.general_segmentation_utils
   :members:

Nuclei Segmentation
-------------------

.. automodule:: image_analysis_3D.segmentation_utils.nuclei_segmentation
   :members:

Cell Segmentation
-----------------

.. automodule:: image_analysis_3D.segmentation_utils.cell_segmentation
   :members:

Segmentation Decoupling
-----------------------

.. automodule:: image_analysis_3D.segmentation_utils.segmentation_decoupling
   :members:

Image Utilities
===============

Image Processing
----------------

.. automodule:: image_analysis_3D.image_utils.image_utils
   :members:

Featurization Utilities
=======================

Area & Size & Shape
-------------------

.. automodule:: image_analysis_3D.featurization_utils.area_size_shape_utils
   :members:

Colocalization
--------------

.. automodule:: image_analysis_3D.featurization_utils.colocalization_utils
   :members:

Granularity
-----------

.. automodule:: image_analysis_3D.featurization_utils.granularity_utils
   :members:
   :private-members:

Intensity
---------

.. automodule:: image_analysis_3D.featurization_utils.intensity_utils
   :members:

Neighbors
---------

.. automodule:: image_analysis_3D.featurization_utils.neighbors_utils
   :members:

Texture
-------

.. automodule:: image_analysis_3D.featurization_utils.texture_utils
   :members:

SAMMED3D Featurizer
-------------------

.. automodule:: image_analysis_3D.featurization_utils.sammed3d_featurizer
   :members:

CHAMMI-75 Featurizer
--------------------

.. automodule:: image_analysis_3D.featurization_utils.chammi75_featurization
   :members:

Feature Writing
---------------

.. automodule:: image_analysis_3D.featurization_utils.feature_writing_utils
   :members:

Resource Profiling
------------------

.. automodule:: image_analysis_3D.featurization_utils.resource_profiling_util
   :members:

Loading Classes
---------------

.. automodule:: image_analysis_3D.featurization_utils.loading_classes
   :members:
   :no-index:

Featurization Errors
--------------------

.. automodule:: image_analysis_3D.featurization_utils.errors
   :members:

Visualization Utilities
=======================

Animation
---------

.. automodule:: image_analysis_3D.visualization_utils.animation_utils
   :members: