Custom Detector

Subclass ObjectDetector to create a detector that writes to objmask and objmap. Operations are pydantic models: declare each parameter as an annotated class-level field — there is no hand-written __init__.

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

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

    Args:
        threshold: Intensity cutoff; pixels above it are marked as colony.
    """

    threshold: float = 0.5

    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