phenotypic.enhance.ContrastStretching#

class phenotypic.enhance.ContrastStretching(lower_percentile: int = 2, upper_percentile: int = 98)[source]

Bases: ImageEnhancer

Stretch the intensity range of detect_mat to fill the full dynamic range.

Rescales pixel values based on lower and upper percentiles, compressing outliers (specular highlights, deep shadows) while expanding the range where colony intensities reside. Simpler and faster than CLAHE, with no local tile artifacts.

Parameters:

  • lower_percentile (int) – Dark clipping point. Pixels below this percentile are mapped to the minimum. Typical range: 1–5. Default: 2.

  • upper_percentile (int) – Bright clipping point. Pixels above this percentile are mapped to the maximum. Typical range: 95–99. Default: 98.

Returns:

Input image with detect_mat rescaled to the full dynamic range. rgb and gray are unchanged.

Return type:

Image

Best For:

  • Plates with narrow histograms (under-exposed or low-contrast).

  • Normalizing exposure across different imaging sessions.

  • Quick preprocessing before global thresholding (Otsu, Triangle).

Consider Also:

  • CLAHE when illumination varies spatially across the plate.

  • HomomorphicFilter when the primary issue is a brightness gradient rather than narrow dynamic range.

See also

How To: Enhance Low-Contrast Images for a comparison of contrast enhancement methods. What Enhancement Actually Does for how enhancement fits into the pipeline model.

Methods

__init__

apply

Applies the operation to an image, either in-place or on a copy.

widget

Return (and optionally display) the root widget.
__init__(lower_percentile: int = 2, upper_percentile: int = 98)[source]
Parameters:

  • lower_percentile (int) – Dark clipping point. Increase to suppress deep shadows/edge artifacts; too high may remove meaningful dark background structure. Typical range: 1–5.

  • upper_percentile (int) – Bright clipping point. Decrease to suppress glare/highlights; too low may flatten bright colonies. Typical range: 95–99.

__del__()

Automatically stop tracemalloc when the object is deleted.

__getstate__()

Prepare the object for pickling by disposing of any widgets.

This ensures that UI components (which may contain unpickleable objects like input functions or thread locks) are cleaned up before serialization.

Note

This method modifies the object state by calling dispose_widgets(). Any active widgets will be detached from the object.

apply(image, inplace=False)

Applies the operation to an image, either in-place or on a copy.

Parameters:

  • image (Image) – The arr image to apply the operation on.

  • inplace (bool) – If True, modifies the image in place; otherwise, operates on a copy of the image.

Returns:

The modified image after applying the operation.

Return type:

Image

widget(image: Image | None = None, show: bool = False) → Widget

Return (and optionally display) the root widget.

Parameters:

  • image (Image | None) – Optional image to visualize. If provided, visualization controls will be added to the widget.

  • show (bool) – Whether to display the widget immediately. Defaults to False.

Returns:

The root widget.

Return type:

ipywidgets.Widget

Raises:

ImportError – If ipywidgets or IPython are not installed.

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