phenotypic.enhance.ContrastStretching#

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

Bases: ImageEnhancer

Contrast stretching for plate images.

Rescales intensities based on chosen lower/upper percentiles so the bulk of pixel values expands to the full display range. For agar plate colony images, this often improves separability between colonies and agar by compressing extreme outliers (e.g., specular highlights, deep shadows) while expanding the dynamic range where colonies reside.

Use cases (agar plates): - Normalize exposure across scans or camera shots before thresholding. - Recover contrast on low-contrast plates without amplifying noise as much as

aggressive histogram equalization might.

  • Prepare images for global methods (e.g., Otsu) or for visualization.

Tuning and effects: - lower_percentile: Increasing this value clips more of the darkest pixels

(e.g., shadows/edge artifacts), which brightens the image and can reveal translucent colonies. Too high can erase true dark background structure.

  • upper_percentile: Decreasing this value clips more highlights (e.g., glare, dust reflections), preventing them from dominating contrast. Too low flattens bright colonies or pigmented regions.

Caveats: - If outliers are biological signals (very bright colonies), heavy clipping can

reduce their apparent intensity and bias measurements.

  • Contrast stretching is global; it will not fix spatially varying illumination on its own (consider GaussianSubtract or RollingBallRemoveBG).

Parameters:

  • lower_percentile (int) – Lower percentile used to define the input range for rescaling. Pixels below this are mapped to the minimum.

  • upper_percentile (int) – Upper percentile used to define the input range for rescaling. Pixels above this are mapped to the maximum.

Methods

__init__

apply

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

dispose_widgets

Drop references to the UI widgets.

sync_widgets_from_state

Push internal state into widgets.

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

dispose_widgets() → None#

Drop references to the UI widgets.

Return type:

None

sync_widgets_from_state() → None#

Push internal state into widgets.

Return type:

None

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.