Explanation
===========

Conceptual material that builds understanding. These pages explain *why* things
work the way they do, discuss tradeoffs and failure modes, and provide the
theoretical background for PhenoTypic's algorithms.

.. toctree::
   :maxdepth: 1
   :caption: Core Concepts

   pipeline_mental_model
   color_spaces_for_phenotyping
   how_the_image_class_works

.. toctree::
   :maxdepth: 1
   :caption: Detection & Processing

   detection_strategies_compared
   grid_vs_non_grid_detection
   what_enhancement_does
   refinement_strategies

.. toctree::
   :maxdepth: 1
   :caption: Measurement & Analysis

   measurement_metrics_biological_meaning
   edge_effects_in_plate_assays
   image_quality_noise_contrast_structure

.. toctree::
   :maxdepth: 1
   :caption: Specialized Topics

   filamentous_fungi_algorithm
   prefab_pipelines_guide