API Reference

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

Image

• Image Class Methods
  • Overview
  • Initialization & Creation
  • Data Access - Grayscale
  • Data Access - RGB
  • Data Access - Enhanced
  • Data Access - Objects (Detection Results)
  • Color Space Operations
  • Visualization & Plotting
  • File I/O
  • Image Manipulation
  • Visualization (Basic Display)
  • Metadata Management
  • Comparison & Utility
• Color Space Operations
  • Image.color
  • CIE XYZ Color Space
  • CIE XYZ under D65 Illuminant
  • CIE L*a*b* Color Space
  • CIE xy Chromaticity
  • HSV Color Space
• Visualization & Plotting
  • Image.plot
  • Morphological Progression Analysis
  • Structural Response Curves
  • Boundary Displacement Analysis
  • Object Size Distribution
  • Size Viewer (Interactive)
  • Spatial Size Distribution Map
  • Size-Intensity Correlation

GridImage

• GridImage Class Methods
  • Overview
  • Initialization & Creation
  • Grid Operations
  • Grid-Based Access
  • Data Access (Inherited from Image)
  • Grid Visualization
  • File I/O (Inherited)
  • Image Manipulation (Inherited)
  • Metadata Management (Inherited)
  • Comparison & Utility (Inherited)

ImagePipeline

• ImagePipeline Class Methods
  • Overview
  • Initialization & Configuration
  • Pipeline Execution
  • Performance Monitoring
  • Serialization & State
  • Batch Processing
  • Comparison & Utility

Reference Pages

• CLI Reference
• Configuration Reference
• Glossary

Modules

phenotypic	A library for processing and analyzing images of microbe colonies on solid media agar.
phenotypic.abc_	Abstract interfaces for fungal colony image operations.
phenotypic.analysis	Analytics for quantified fungal colony plates.
phenotypic.correction	Image/grid correction for agar plate captures.
phenotypic.data	Sample and synthetic agar plate images for fungal colony testing.
phenotypic.detect	Colony/object detectors for agar plate images.
phenotypic.enhance	Image enhancers to boost fungal colonies on agar backgrounds.
phenotypic.grid	Grid discovery for plated fungal colonies.
phenotypic.measure	Feature extraction from detected fungal colonies.
phenotypic.prefab	Prefab pipelines for fungal colony plate processing.
phenotypic.refine	Mask refinement for detected fungal colonies.
phenotypic.tools_	Developer tools shared across fungal colony plate workflows.
phenotypic.util	A module for useful utility operations and functions that don't fit into a specific category.