Utilizing the output JSON file

[merihdeniz19]

I was wondering how can we utilize the output JSON file to get information regarding the nucleus elongation, area, minimum/maximum diameter information. I checked the example jupyter notebook but it was still not clear to me how to get this information from the JSON file for the whole wsi image. Thank you so much in advance!

[simongraham]

The usage.py example notebook will tell you how to get the nuclei contour coordinates. When you have the contour coordinates, you can use opencv to get the sort of features that you are referring to. Consider using a function like this:

def get_contour_feats(cnt):
    """Get morphological features from input contours."""

    # calculate some things useful later:
    m = cv2.moments(cnt)

    # ** regionprops **
    Area = m["m00"]

    Perimeter = cv2.arcLength(cnt, True)
    # bounding box: x,y,width,height
    BoundingBox = cv2.boundingRect(cnt)
    # centroid    = m10/m00, m01/m00 (x,y)
    Centroid = (m["m10"] / m["m00"], m["m01"] / m["m00"])

    # EquivDiameter: diameter of circle with same area as region
    EquivDiameter = np.sqrt(4 * Area / np.pi)
    # Extent: ratio of area of region to area of bounding box
    Extent = Area / (BoundingBox[2] * BoundingBox[3])

    # CONVEX HULL 
    # convex hull vertices
    ConvexHull = cv2.convexHull(cnt)
    ConvexArea = cv2.contourArea(ConvexHull)
    # Solidity := Area/ConvexArea
    Solidity = Area / ConvexArea

    # ELLIPSE - determine best-fitting ellipse.
    centre, axes, angle = cv2.fitEllipse(cnt)
    MAJ = np.argmax(axes)  # this is MAJor axis, 1 or 0
    MIN = 1 - MAJ  # 0 or 1, MINor axis
    # Note: axes length is 2*radius in that dimension
    MajorAxisLength = axes[MAJ]
    MinorAxisLength = axes[MIN]
    Eccentricity = np.sqrt(1 - (axes[MIN] / axes[MAJ]) ** 2)
    Orientation = angle
    EllipseCentre = centre  # x,y

    return {
        "area": Area,
        "perimeter": Perimeter,
        "equiv-diameter": EquivDiameter,
        "extent": Extent,
        "convex-area": ConvexArea,
        "solidity": Solidity,
        "major-axis-length": MajorAxisLength,
        "minor-axis-length": MinorAxisLength,
        "eccentricity": Eccentricity,
        "orientation": Orientation,
        "ellipse-centre-x": EllipseCentre[0],
        "ellipse-centre-y": EllipseCentre[1],
    }

[merihdeniz19]

Thank you so much!