from __future__ import annotations
from typing import TYPE_CHECKING, overload
if TYPE_CHECKING:
from phenotypic._core._image import Image
from phenotypic._core._grid_image import GridImage
from ._image_operation import ImageOperation
from phenotypic.sdk_.funcs_ import validate_operation_integrity
from abc import ABC, abstractmethod
# <<Interface>>
[docs]
class ObjectDetector(ImageOperation, ABC):
"""Abstract base class for colony detection operations on agar plate images.
ObjectDetector defines the interface for algorithms that identify and label microbial
colonies (or other objects) in image data. Detection is a critical step in the PhenoTypic
image processing pipeline: it bridges image preprocessing (enhancement) and downstream
analysis (measurement, refinement, and statistical analysis).
**Quick Decision Guide**
Use this guide to choose the right operation for your task:
- **ObjectDetector:** Implementing a novel detection algorithm? Produces both objmask
(binary) and objmap (labeled).
- **ThresholdDetector:** Your algorithm converts intensity to binary via thresholding?
Subclass ThresholdDetector for specialized threshold strategies.
- **ImageEnhancer:** Need to preprocess image data (blur, contrast, denoise) before
detection? Use enhancement to prepare detect_mat for better detection.
- **ObjectRefiner:** Need to clean up *existing* masks (size filter, morphology, merge)?
Refiner operates on objmask/objmap without analyzing image data.
- **Threshold vs Edge vs Peak:** Threshold works when intensity separates colonies from
background; edge-based (Canny) finds boundaries; peak-based assumes circular shapes.
- **Grid-aware analysis:** Processing arrayed plates? Use GridObjectRefiner or
GridFinder for well-plate-specific logic.
**What does ObjectDetector do?**
ObjectDetector subclasses analyze image data and produce two outputs that describe detected
colonies:
- **image.objmask** (binary mask): A 2D boolean array where True indicates colony pixels
and False indicates background. Each True pixel belongs to *some* colony but the mask
does not distinguish which colony each pixel belongs to—that is the role of objmap.
- **image.objmap** (labeled map): A 2D integer array where each pixel value identifies the
colony it belongs to. Background is 0, and each unique positive integer (1, 2, 3, ...,
N) represents a distinct labeled colony. This enables accessing individual colonies
via ``image.objects`` after detection.
**Key principle: ObjectDetector is READ-ONLY for image data**
ObjectDetector operations:
- **Read** ``image.detect_mat[:]`` (detection matrix), ``image.rgb[:]``, and optionally
other image data to inform detection.
- **Write** only ``image.objmask[:]`` and ``image.objmap[:]``.
- **Protect** ``image.rgb``, ``image.gray``, and ``image.detect_mat`` via automatic integrity
validation (``@validate_operation_integrity`` decorator).
Any attempt to modify protected image components raises ``OperationIntegrityError`` when
``phenotypic.settings.VALIDATE_OPS`` is true (enabled during development/testing).
**Why is detection central to the pipeline?**
Detection enables:
1. **Object identification:** Distinguishes individual colonies from background and from
each other.
2. **Downstream analysis:** Once colonies are labeled, ``image.objects`` provides access
to properties (area, intensity, centroid, morphology) for each colony.
3. **Refinement:** ObjectRefiner operations clean up detection masks/maps post-detection
(e.g., removing spurious objects, merging fragments, filtering by size).
4. **Phenotyping:** Measurement operations (MeasureFeatures) extract colony features
(color, morphology, growth) for statistical analysis.
**Differences: objmask vs objmap**
- **objmask (binary):** Answers "is this pixel part of *any* colony?" Simple, useful for
visualization or as input to further processing (e.g., morphological operations).
Generated by most detectors via thresholding or edge detection.
- **objmap (labeled):** Answers "which colony does this pixel belong to?" Enables per-object
analysis. Each colony has a unique integer label, and connected-component labeling
(usually ``scipy.ndimage.label``) assigns these labels.
Both are typically set together in ``_operate()`` via::
image.objmask[:] = binary_mask
image.objmap[:] = labeled_map
**When to use ObjectDetector vs ThresholdDetector vs ObjectRefiner**
- **ObjectDetector (this class):** Implement when you have a novel algorithm that produces
both objmask and objmap from image data. Examples: [OtsuDetector](src/phenotypic/detect/_otsu_detector.py),
[CannyDetector](src/phenotypic/detect/_canny_detector.py), [RoundPeaksDetector](src/phenotypic/detect/_round_peaks_detector.py),
[WatershedDetector](src/phenotypic/detect/_watershed_detector.py).
- **ThresholdDetector (ObjectDetector subclass):** Inherit from this if your detection
relies on a threshold value. Provides common patterns and signals intent. Examples:
[OtsuDetector](src/phenotypic/detect/_otsu_detector.py), [LiDetector](src/phenotypic/detect/_li_detector.py),
[YenDetector](src/phenotypic/detect/_yen_detector.py), [TriangleDetector](src/phenotypic/detect/_triangle_detector.py).
- **ObjectRefiner (different ABC):** Use when modifying existing masks/maps without
analyzing image data. Examples: size filtering, morphological cleanup, erosion/dilation,
merging nearby objects, removing objects near borders.
**How to implement a custom ObjectDetector**
1. **Create the class:**
.. code-block:: python
from phenotypic.abc_ import ObjectDetector
from phenotypic import Image
class MyDetector(ObjectDetector):
param1: float # Annotated class-level fields
param2: int = 10
def _operate(self, image: Image) -> Image:
# Detection logic here
return image
2. **Within _operate(), read image data carefully:**
- Access via accessors: ``image.detect_mat[:]``, ``image.gray[:]``, ``image.rgb[:]``
- Never modify these; integrity validation will catch it
- Consider the data type and range (uint8, uint16, float, etc.)
3. **Perform detection:** Use your algorithm to create a binary mask and labeled map.
Typical approaches:
- **Thresholding-based:** Global or local threshold → binary mask → label (see [OtsuDetector](src/phenotypic/detect/_otsu_detector.py))
- **Edge-based:** Edge detector (Canny) → invert edges → label regions (see [CannyDetector](src/phenotypic/detect/_canny_detector.py))
- **Peak-based:** Detect intensity peaks → grow regions → label (see [RoundPeaksDetector](src/phenotypic/detect/_round_peaks_detector.py))
- **Region-based:** Watershed or morphological operations (see [WatershedDetector](src/phenotypic/detect/_watershed_detector.py))
4. **Create and set the binary mask and labeled map:**
.. code-block:: python
from scipy import ndimage
import numpy as np
# Example: simple Otsu thresholding
enh = image.detect_mat[:]
threshold = skimage.filters.threshold_otsu(enh)
binary_mask = enh > threshold
# Remove small noise
binary_mask = skimage.morphology.remove_small_objects(binary_mask, min_size=20)
# Label connected components
labeled_map, num_objects = ndimage.label(binary_mask)
# Set both outputs
image.objmask[:] = binary_mask
image.objmap[:] = labeled_map
return image
5. **Post-processing (optional):** Some detectors include additional cleanup:
- **Morphological operations:** Apply erosion, dilation, opening, or closing to refine
mask topology (remove noise, bridge fragments, smooth boundaries).
- **Clear borders:** Use ``skimage.segmentation.clear_border()`` to remove objects
touching image edges.
- **Remove small/large objects:** Use ``skimage.morphology.remove_small_objects()`` or
``skimage.morphology.remove_large_objects()`` to filter by area.
- **Relabel:** Call ``image.objmap.relabel(connectivity=...)`` to ensure consecutive
labels.
**Helper functions from scipy and scikit-image**
Common utilities for ObjectDetector implementations:
- **scipy.ndimage.label():** Assigns unique integers to connected components in a binary
mask. Returns (labeled_array, num_features). Specify ``structure`` for connectivity
(default 3x3 with all 8 neighbors; use ``generate_binary_structure(2, 1)`` for
4-connectivity).
- **skimage.morphology.remove_small_objects():** Removes binary regions smaller than
min_size pixels. Helpful for filtering noise or spurious detections.
- **skimage.morphology.remove_large_objects():** Removes regions larger than a threshold.
Useful for excluding large artefacts or plate boundaries.
- **skimage.segmentation.clear_border():** Sets pixels on the image border to False,
eliminating objects that touch the edge (common in arrayed imaging where wells at
plate boundaries may be partially cut off).
- **skimage.morphology.binary_opening():** Erosion followed by dilation; removes small
noise while preserving larger objects. Use with a suitable shape (disk, square, or
diamond).
- **scipy.ndimage.binary_dilation() / binary_erosion():** Expand or shrink objects
morphologically. Useful for bridging fragmented colonies or removing small protrusions.
- **skimage.feature.canny():** Multi-stage edge detection (Gaussian → gradient → non-max
suppression → hysteresis). Robust but requires threshold tuning.
**Reference implementations in PhenoTypic**
Study these implementations to learn detection patterns:
- [OtsuDetector](src/phenotypic/detect/_otsu_detector.py): Simple thresholding with global
Otsu method
- [HysteresisDetector](src/phenotypic/detect/_hysteresis_detector.py): Advanced dual-threshold
with edge tracking (excellent reference for complex detection)
- [CannyDetector](src/phenotypic/detect/_canny_detector.py): Edge-based detection with
connectivity cleanup
- [RoundPeaksDetector](src/phenotypic/detect/_round_peaks_detector.py): Peak-based approach
for round colonies
- [WatershedDetector](src/phenotypic/detect/_watershed_detector.py): Region-based segmentation
**When and how to refine detections (post-processing)**
Raw detections often need cleanup:
- **Remove small noise:** Spurious single-pixel detections or tiny salt-and-pepper artifacts.
Use ObjectRefiner + remove_small_objects.
- **Clean borders:** Colonies at plate edges may be incomplete. Use ObjectRefiner or
clear_border() in detector.
- **Merge fragments:** Noise or uneven lighting can fragment a single colony into multiple
labels. Use ObjectRefiner with morphological dilation or connected-component merging.
- **Remove large objects:** Plate edges, dust on the scanner, or agar artifacts appear
as large regions. Use ObjectRefiner + remove_large_objects.
- **Grid-aware filtering:** In arrayed formats (96-well, 384-well), one object per grid
cell is expected. Use GridObjectRefiner to enforce this constraint or GridRefiner to
assign dominant objects to grid positions.
Example pipeline with detection + refinement::
from phenotypic import Image, ImagePipeline
from phenotypic.detect import OtsuDetector
from phenotypic.refine import RemoveSmallObjectsRefiner, ClearBorderRefiner
pipeline = ImagePipeline()
pipeline.add(OtsuDetector()) # Initial detection
pipeline.add(ClearBorderRefiner()) # Remove edge-touching objects
pipeline.add(RemoveSmallObjectsRefiner(min_size=100)) # Filter noise
image = Image("plate.jpg")
result = pipeline.operate([image])[0]
# result now has clean, labeled colonies ready for measurement
Attributes:
None (all operation parameters are stored in subclass instances).
Methods:
apply(image, inplace=False): User-facing method to apply detection to an image.
Handles copy/inplace logic and parameter matching.
_operate(image, **kwargs): Abstract instance method implemented by subclasses
with detection logic. Must set image.objmask and image.objmap.
Notes:
- **Integrity protection:** The @validate_operation_integrity decorator on apply()
ensures image.rgb, image.gray, and image.detect_mat are not modified. Violations
raise OperationIntegrityError during development (VALIDATE_OPS=True).
- **Binary mask is often intermediate:** Many implementations create objmask first,
then derive objmap via connected-component labeling. Both must be set for
downstream code to work correctly.
- **Label consistency:** Use image.objmap.relabel() after manipulating the labeled
map to ensure labels are consecutive (1, 2, 3, ..., N) and to update objmask.
- **Memory efficiency:** Large images and detailed segmentations consume memory.
Consider inplace=True in pipelines processing many images, or use sparse
representations (objmap uses scipy.sparse internally).
- **Instance _operate() method:** Access parameters via ``self`` attributes.
Examples:
Detect colonies in a plate image and access results:
>>> from phenotypic import Image
>>> from phenotypic.detect import OtsuDetector
>>> # Load a plate image
>>> plate = Image("agar_plate.jpg")
>>> # Apply detection
>>> detector = OtsuDetector()
>>> detected = detector.apply(plate)
>>> # Access binary mask
>>> mask = detected.objmask[:] # numpy array
>>> print(f"Mask shape: {mask.shape}, True pixels: {mask.sum()}")
>>> # Access labeled map
>>> objmap = detected.objmap[:]
>>> print(f"Detected {objmap.max()} colonies")
>>> # Iterate over colonies and measure properties
>>> for colony in detected.objects:
... print(f"Colony area: {colony.area} px, "
... f"centroid: {colony.centroid}")
Detection in a full pipeline with enhancement and refinement:
>>> from phenotypic import Image, ImagePipeline
>>> from phenotypic.enhance import GaussianBlur
>>> from phenotypic.detect import CannyDetector
>>> from phenotypic.refine import RemoveSmallObjectsRefiner
>>> from phenotypic.measure import MeasureColor
>>> # Create a processing pipeline
>>> pipeline = ImagePipeline()
>>> pipeline.add(GaussianBlur(sigma=2.0)) # Preprocessing
>>> pipeline.add(CannyDetector(sigma=1.5)) # Detection
>>> pipeline.add(RemoveSmallObjectsRefiner(min_size=50)) # Cleanup
>>> pipeline.add(MeasureColor()) # Downstream analysis
>>> # Load image and process
>>> image = Image("plate.jpg")
>>> result = pipeline.operate([image])[0]
>>> # Results include enhanced image, detected/refined colonies, and measurements
>>> print(f"Colonies: {result.objmap[:].max()}")
>>> print(f"Measurements: {result.measurements.shape}")
"""
@overload
def apply(self, image: GridImage, inplace: bool = False) -> GridImage: ...
@overload
def apply(self, image: Image, inplace: bool = False) -> Image: ...
[docs]
@validate_operation_integrity("image.rgb", "image.gray", "image.detect_mat")
def apply(self, image: Image, inplace=False) -> Image:
return super().apply(image=image, inplace=inplace)
[docs]
@abstractmethod
def _operate(self, image: Image) -> Image:
return image
