phenotypic.data#

Sample and synthetic agar plate images for fungal colony testing.

Provides loaders and generators for representative plate scenes used in demos, benchmarks, and tests: synthetic single colonies, synthetic full plates, time-course captures at 12–72 hours, early low-contrast crops, and smear-plate examples. Utilities return arrays or ready-to-use Image/GridImage objects for rapid pipeline trials.

Functions

load_synthetic_colony

Loads synthetic colony data from a pre-saved file.

load_synth_yeast_plate

Returns a phenotypic.GridImage of a synthetic plate with the colonies detected

make_synthetic_colony

Generate a single bright fungal colony on solid-media agar.

make_synthetic_plate

Generate a synthetic array plate with multiple circular colonies.

make_synthetic_filamentous_plate

Generate a synthetic plate with filamentous (hairy/branching) colonies.

load_plate_12hr

Returns a plate image of a K.

load_plate_72hr

Return a image of a k.

load_plate_series

Return a series of plate images across 6 time samples

load_early_colony

Returns a colony image array of K.

load_faint_early_colony

Returns a faint colony image array of K.

load_colony

Returns a colony image array of K.

load_smear_plate_12hr

Returns a plate image array of K.

load_smear_plate_24hr

Returns a plate image array of K.

load_yeast_plate

Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.

load_fungi_plate

Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.

load_yeast_plate_full

Load a full (uncropped) Rhodotorula yeast plate image with color checker.

load_fungi_plate_full

Load a full (uncropped) Neurospora filamentous fungi plate image with color checker.
phenotypic.data.load_colony(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a colony image array of K. Marxianus at 72 hrs

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_early_colony(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a colony image array of K. Marxianus at 12 hrs

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_faint_early_colony(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a faint colony image array of K. Marxianus at 12 hrs

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_fungi_plate(mode: Literal['array', 'Image', 'GridImage'] = 'GridImage') → np.ndarray | Image | GridImage[source]

Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.

Returns a pre-cropped plate image of Neurospora filamentous fungi arranged in a 96-well grid. Irregular hyphal morphology with spreading growth – suitable for filamentous fungi tutorials and how-to guides.

Parameters:

mode (Literal['array', 'Image', 'GridImage']) – Return format. Default: 'GridImage'.

Returns:

The plate image in the requested format.

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_fungi_plate_full(mode: Literal['array', 'Image', 'GridImage'] = 'Image') → np.ndarray | Image | GridImage[source]

Load a full (uncropped) Neurospora filamentous fungi plate image with color checker.

Returns the full plate image including scanner margins and a color checker target. Use for fungi-specific correction workflow tutorials.

Parameters:

mode (Literal['array', 'Image', 'GridImage']) – Return format. Default: 'Image'.

Returns:

The full plate image in the requested format.

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_plate_12hr(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a plate image of a K. Marxianus colony 96 array plate at 12 hrs

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_plate_72hr(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Return a image of a k. marxianus colony 96 array plate at 72 hrs

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_plate_series(mode: Literal['array', 'Image', 'GridImage'] = 'array') → List[np.ndarray | Image | GridImage][source]

Return a series of plate images across 6 time samples

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

List[Union[np.ndarray, Image, GridImage]]

phenotypic.data.load_smear_plate_12hr(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a plate image array of K. Marxianus that contains noise such as smears

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_smear_plate_24hr(mode: Literal['array', 'Image', 'GridImage'] = 'array') → np.ndarray | Image | GridImage[source]

Returns a plate image array of K. Marxianus that contains noise such as smears

Parameters:

mode (Literal['array', 'Image', 'GridImage'])

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_synth_yeast_plate()[source]

Returns a phenotypic.GridImage of a synthetic plate with the colonies detected

phenotypic.data.load_synthetic_colony(mode: Literal['array', 'Image'] = 'array') → numpy.ndarray | Image[source]

Loads synthetic colony data from a pre-saved file.

Parameters:

mode (Literal['array', 'Image'])

Return type:

numpy.ndarray | Image

phenotypic.data.load_yeast_plate(mode: Literal['array', 'Image', 'GridImage'] = 'GridImage') → np.ndarray | Image | GridImage[source]

Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.

Returns a pre-cropped plate image of Neurospora filamentous fungi arranged in a 96-well grid. Irregular hyphal morphology with spreading growth – suitable for filamentous fungi tutorials and how-to guides.

Parameters:

mode (Literal['array', 'Image', 'GridImage']) – Return format. Default: 'GridImage'.

Returns:

The plate image in the requested format.

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.load_yeast_plate_full(mode: Literal['array', 'Image', 'GridImage'] = 'Image') → np.ndarray | Image | GridImage[source]

Load a full (uncropped) Rhodotorula yeast plate image with color checker.

Returns the full plate image including scanner margins and a color checker target. Use for tutorials and how-to guides that demonstrate cropping (ImageCropper), padding (ImagePadder), vignetting correction (VignetteCorrector), or color correction (ColorCorrector).

Parameters:

mode (Literal['array', 'Image', 'GridImage']) – Return format. Default: 'Image'.

Returns:

The full plate image in the requested format.

Return type:

Union[np.ndarray, Image, GridImage]

phenotypic.data.make_synthetic_colony(h: int = 256, w: int = 256, bit_depth: int = 8, colony_rgb: Tuple[float, float, float] = (0.96, 0.88, 0.82), agar_rgb: Tuple[float, float, float] = (0.55, 0.56, 0.54), seed: int = 1) → numpy.ndarray[source]

Generate a single bright fungal colony on solid-media agar.

Parameters:
Return type:

numpy.ndarray

phenotypic.data.make_synthetic_filamentous_plate(nrows: int = 8, ncols: int = 12, plate_h: int = 2048, plate_w: int = 3072, bit_depth: int = 8, colony_rgb: Tuple[float, float, float] = (0.96, 0.9, 0.85), agar_rgb: Tuple[float, float, float] = (0.55, 0.56, 0.54), seed: int = 1, spacing_factor: float = 0.85, colony_size_variation: float = 0.15, filament_density: float = 100.0, filament_reach: float = 2.2) → numpy.ndarray[source]

Generate a synthetic plate with filamentous (hairy/branching) colonies.

Parameters:
Return type:

numpy.ndarray

phenotypic.data.make_synthetic_plate(nrows: int = 8, ncols: int = 12, plate_h: int = 2048, plate_w: int = 3072, bit_depth: int = 8, colony_rgb: Tuple[float, float, float] = (0.96, 0.88, 0.82), agar_rgb: Tuple[float, float, float] = (0.55, 0.56, 0.54), seed: int = 1, spacing_factor: float = 0.85, colony_size_variation: float = 0.15) → numpy.ndarray[source]

Generate a synthetic array plate with multiple circular colonies.

Parameters:
Return type:

numpy.ndarray

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