phenotypic.refine.GridOversizedObjectRemover#

class phenotypic.refine.GridOversizedObjectRemover(*args, **kwargs)[source]

Bases: GridObjectRefiner

Remove objects whose bounding box exceeds the maximum grid cell dimension.

Compares each object’s width and height against the largest cell span in the grid and discards objects that match or exceed it. Eliminates merged colonies, agar rim intrusions, and segmentation spillover that span entire grid cells.

Returns:

Input image with objmap and objmask updated to exclude objects exceeding the grid cell size.

Return type:

Image

Best For:

  • Dropping merged blobs that span adjacent grid positions.

  • Removing strong edge artifacts near the plate rim that intrude into the grid.

  • Post-detection cleanup on pinned colony grids where each cell should contain one confined colony.

Consider Also:

See also

How To: Refine Noisy Detection Boundaries for grid-based refinement workflows. Refinement Strategies for an overview of grid refinement strategies.

Methods

__init__

apply

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

widget

Return (and optionally display) the root widget.
__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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