Glossary

accessor

A property on Image that provides NumPy-style indexing to image data. Primary accessors: rgb, gray, detect_mat, objmask, objmap. High-level accessors: color, grid, metadata, plot.

colony

A visible microbial growth on an agar plate surface. In PhenoTypic, a colony corresponds to a connected component in the object map.

detect_mat

The detection matrix — an enhanced grayscale representation of the plate image that detectors consume. Enhancers modify detect_mat while leaving rgb and gray unchanged.

grid section

A rectangular region of a GridImage corresponding to one well in the physical plate. Indexed by (row, column) or flattened section number.

GridImage

An Image subclass that adds grid awareness — row/column layout, section extraction, and grid-aware detection/refinement. Use for arrayed colony plates (96-well, 384-well).

hyphae

Branching filamentous structures produced by filamentous fungi. Singular: hypha. The network of hyphae is called mycelium.

Image

PhenoTypic’s central data structure. Stores pixel data (rgb, gray), detection results (objmask, objmap), metadata, and provides accessor- based access to all components.

ImagePipeline

A serializable chain of operations (enhancers, detectors, refiners) and measurements. Apply to images with .apply() or .apply_and_measure(). Save/load with .to_json() / .from_json().

inoculum

The initial microbial deposit on the agar surface. In filamentous fungi detection, the dense central region from which hyphae radiate.

mycelium

The network of branching hyphae that forms the body of a filamentous fungus. Detected by FilamentousFungiDetector.

objmap

The labeled object map — a uint16 array where each detected colony receives a unique integer label (0 = background). Written by detectors, refined by refiners.

objmask

The binary object mask — a boolean array where True indicates colony pixels and False indicates background. Written by detectors, refined by refiners.

prefab pipeline

A pre-configured ImagePipeline subclass tuned for a specific organism or imaging scenario (e.g., HeavyOtsuPipeline, FilamentousFungiPipeline).

well

A physical position on an arrayed agar plate (e.g., one of 96 positions in a 96-well format). Corresponds to a grid section in PhenoTypic.