phenotypic.correction#

Image/grid correction for agar plate captures.

Offers operations that realign grids or correct field-of-view drift so detected colonies stay anchored to their intended wells or pins. The grid aligner adjusts spacing and offsets using reference points or heuristics suited to arrayed plate layouts.

Classes

GridAligner

Calculates the optimal gridding orientation based on the alignment of the objects in the image and rotates the image accordingly.
class phenotypic.correction.GridAligner(axis: int = 0, mode: str = 'edge')[source]#

Bases: GridCorrector

Calculates the optimal gridding orientation based on the alignment of the objects in the image and rotates the image accordingly.

This class inherits from GridCorrector and is designed to calculate the optimal gridding orientation. This is used to align the image, and helps to improve the quality of automated gridding results. It’s highly recommended to redetect objects in the image after alignment.

Parameters:
__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: GridImage, inplace=False) → GridImage#

Calculates the optimal rotation angle and applies it to a grid image for alignment along the specified axis.

The method performs alignment of a GridImage object along either nrows or columns based on the specified axis. It calculates the linear regression slope and intercept for the axis, determines geometric properties of the grid vertices, and computes rotation angles needed to align the image. The optimal angle is found by minimizing the error across all computed angles, and the image is rotated accordingly.

Raises:

ValueError – If the axis is not 0 (row-wise) or 1 (column-wise).

Parameters:

image (ImageGridHandler) – The arr grid image object to be aligned.

Returns:

The rotated grid image object after alignment.

Return type:

ImageGridHandler

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.