Custom Detector

Subclass ObjectDetector to create a detector that writes to objmask and objmap.

from phenotypic.abc_ import ObjectDetector
import numpy as np
from skimage.measure import label

class MyDetector(ObjectDetector):
    """Detect colonies using a fixed intensity threshold."""

    def __init__(self, threshold: float = 0.5):
        self.threshold = threshold

    def _operate(self, image):
        mask = image.detect_mat[:] > self.threshold
        image.objmask[:] = mask
        image.objmap[:] = label(mask).astype(np.uint16)
        return image

Contract

• Read from detect_mat

• Write to objmask (bool) and objmap (uint16 labeled array)

• Do not modify rgb, gray, or detect_mat

• Return the modified image