2D Peak Detection

DataLab provides a “2D Peak Detection” feature which is based on a minimum-maximum filter algorithm.

2D peak detection parameters.

How to use the feature:

• Create or open an image in DataLab workspace

• Select “2d peak detection” in “Analysis” menu

• Enter parameters “Neighborhoods size” and “Relative threhold”

• Optionally, enable “Create regions of interest” to automatically create ROIs around each detected peak:

  • Choose ROI geometry: “Rectangle” or “Circle”

  • ROI size is automatically calculated based on the minimum distance between detected peaks (to avoid overlap)

  • This feature requires at least 2 detected peaks

  • Created ROIs can be useful for subsequent processing on each peak area (e.g., contour detection, measurements, etc.)

2d peak detection results (see test “peak2d_app.py”)

Results are shown in a table:

• Each row is associated to a detected peak

• First column shows the ROI index (0 if no ROI is defined on input image)

• Second and third columns show peak coordinates

Example of 2D peak detection.

The 2d peak detection algorithm works in the following way:

• First, the minimum and maximum filtered images are computed using a sliding window algorithm with a user-defined size (implementation based on scipy.ndimage.minimum_filter and scipy.ndimage.maximum_filter)

• Then, the difference between the maximum and minimum filtered images is clipped at a user-defined threshold

• Resulting image features are labeled using scipy.ndimage.label

• Peak coordinates are then obtained from labels center

• Duplicates are eventually removed

The 2d peak detection parameters are the following:

• “Neighborhoods size”: size of the sliding window (see above)

• “Relative threshold”: detection threshold

• “Create regions of interest”: if enabled, automatically creates ROIs around each detected peak (requires at least 2 peaks)

• “ROI geometry”: shape of the ROIs (“Rectangle” or “Circle”)

Feature is based on get_2d_peaks_coords function from sigima.tools module:

@check_2d_array(non_constant=True)
def get_2d_peaks_coords(
    data: np.ndarray, size: int | None = None, level: float = 0.5
) -> np.ndarray:
    """Detect peaks in image data, return coordinates.

    If neighborhoods size is None, default value is the highest value
    between 50 pixels and the 1/40th of the smallest image dimension.

    Detection threshold level is relative to difference
    between data maximum and minimum values.

    Args:
        data: Input data
        size: Neighborhood size (default: None)
        level: Relative level (default: 0.5)

    Returns:
        Coordinates of peaks
    """
    if size is None:
        size = max(min(data.shape) // 40, 50)
    data_max = spi.maximum_filter(data, size)
    data_min = spi.minimum_filter(data, size)
    data_diff = data_max - data_min
    diff = (data_max - data_min) > get_absolute_level(data_diff, level)
    maxima = data == data_max
    maxima[diff == 0] = 0
    labeled, _num_objects = spi.label(maxima)
    slices = spi.find_objects(labeled)
    coords = []
    for dy, dx in slices:
        x_center = int(0.5 * (dx.start + dx.stop - 1))
        y_center = int(0.5 * (dy.start + dy.stop - 1))
        coords.append((x_center, y_center))
    if len(coords) > 1:
        # Eventually removing duplicates
        dist = distance_matrix(coords)
        for index in reversed(np.unique(np.where((dist < size) & (dist > 0))[1])):
            coords.pop(index)
    return np.array(coords)