delta.utilities.singlecell_features

delta.utilities.singlecell_features(contour: ndarray, mask: ndarray[Any, dtype[uint8]], features: Tuple[str, ...] = ('length', 'width', 'area', 'perimeter', 'edges'), fluo_frames: Optional[ndarray] = None, roi_box: Optional[CroppingBox] = None) → Dict[str, Any]

Extract features for a single cell

Parameters

contourlist

Single cell contour from cv2 findcontours.

mask2D numpy array of bool

Mask of the region to extract (typically a single cell).

featureslist of str, optional

Features to extract. Valid features are ‘length’,’width’,’area’, ‘perimeter’,’edges’,’fluo1’,’fluo2’,…,’fluoN’. The default is (‘length’,’width’,’area’,’perimeter’,’edges’).

fluo_frames3D array, optional

Fluorescent images to extract fluo from. Dimensions are (channels, size_y, size_x). The default is None.

roi_boxdict, optional

Cropping box dictionary (see cropbox())to apply shift when looking at full-frame fluo images. The default is None.

Returns

features_dictdict

Dictionary of requested features.

Raises

ValueError

If the number of fluo frames provided is different from the number of fluo features to extract.