phenotypic.refine.BorderObjectRemover#

class phenotypic.refine.BorderObjectRemover(border_size: int | float | None = 1)[source]

Bases: ObjectRefiner

Remove colonies that touch the image border within a configurable margin.

Zeroes any labeled objects in objmap whose pixels fall within a border band, ensuring only fully contained colonies are analyzed. Partial edge colonies bias size and shape measurements.

Parameters:

border_size (Optional[Union[int, float]]) – Width of the exclusion border. None uses 1% of the smaller dimension. Float in (0, 1) is a fraction of the image size. Int or float >= 1 is absolute pixels. Default: 1.

Returns:

Input image with objmask and objmap updated to exclude border-touching objects.

Return type:

Image

Raises:

TypeError – If border_size type is invalid.

Best For:

  • Plates where the plate rim or image crop truncates edge colonies.

  • Grid assays where border wells are partially visible.

  • Automated crops that shift between frames.

Consider Also:

See also

How To: Refine Noisy Detection Boundaries for a walkthrough of refinement operations. Refinement Strategies for choosing the right refinement sequence.

Methods

__init__

Initialize the remover.

apply

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

widget

Return (and optionally display) the root widget.
__init__(border_size: int | float | None = 1)[source]

Initialize the remover.

Parameters:

border_size (int | float | None) –

Width of the exclusion border around the image.

  • None: Use a default margin equal to 1% of the smaller image dimension.

  • float in (0, 1): Interpret as a fraction of the minimum image dimension, producing a resolution-adaptive margin.

  • int or float ≥ 1: Interpret as an absolute number of pixels.

Notes

Larger margins remove more edge-touching colonies and are useful when crops are loose or the plate rim intrudes. Smaller margins preserve edge colonies but risk including partial objects.

__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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