API Reference#

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

Image#

Image([arr, name, bit_depth, ...])

Comprehensive image processing class with integrated data, color, and I/O management.

`Image.rgb`	Returns the ImageArray accessor; An image rgb represents the multichannel information
`Image.gray`	The image's grayscale representation.
`Image.enh_gray`	Returns the image's enhanced grayscale accessor.
`Image.objmask`	Returns the ObjectMask Accessor; The object mask is a mutable binary representation of the objects in an image to be analyzed.
`Image.objmap`	Returns the ObjectMap accessor; The object map is a mutable integer gray that identifies the different objects in an image to be analyzed.
`Image.objects`	Accessor for performing operations on detected objects in the image.
`Image.color`	Access all color space representations through a unified interface.

GridImage([arr, name, grid_finder, nrows, ...])

A specialized Image object that supports grid-based processing and overlay visualization.

Returns the GridAccessor object for grid-related operations.

`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.