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import numpy as np |
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import cv2 |
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import pandas as pd |
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from scipy import ndimage as ndi |
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from skimage.segmentation import watershed |
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from skimage.feature import peak_local_max |
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from skimage.measure import label, regionprops |
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from .config import Config |
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class ImageProcessor: |
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@staticmethod |
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def macenko_normalize(img, Io=240, alpha=1, beta=0.15): |
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"""Normalizes H&E staining appearance.""" |
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try: |
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HER = np.array([[0.650, 0.704, 0.286], [0.072, 0.990, 0.105], [0.268, 0.570, 0.776]]) |
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h, w, c = img.shape |
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img_flat = img.reshape((-1, 3)) |
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OD = -np.log((img_flat.astype(float) + 1) / Io) |
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ODhat = OD[np.all(OD > beta, axis=1)] |
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if len(ODhat) < 10: return img |
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eigvals, eigvecs = np.linalg.eigh(np.cov(ODhat.T)) |
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That = ODhat.dot(eigvecs[:, 1:3]) |
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phi = np.arctan2(That[:, 1], That[:, 0]) |
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minPhi = np.percentile(phi, alpha) |
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maxPhi = np.percentile(phi, 100 - alpha) |
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vMin = eigvecs[:, 1:3].dot(np.array([(np.cos(minPhi), np.sin(minPhi))]).T) |
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vMax = eigvecs[:, 1:3].dot(np.array([(np.cos(maxPhi), np.sin(maxPhi))]).T) |
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if vMin[0] > vMax[0]: HE = np.array((vMin[:, 0], vMax[:, 0])).T |
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else: HE = np.array((vMax[:, 0], vMin[:, 0])).T |
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Y = np.reshape(OD, (-1, 3)).T |
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C = np.linalg.lstsq(HE, Y, rcond=None)[0] |
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maxC = np.array([1.9705, 1.0308]) |
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Inorm = Io * np.exp(-np.dot(HER[:, 0:2], (C/maxC * maxC)[:, np.newaxis])) |
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return np.clip(np.reshape(Inorm.T, (h, w, c)), 0, 255).astype(np.uint8) |
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except: |
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return img |
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@staticmethod |
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def adaptive_watershed(pred_nuc, pred_con): |
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"""Separates touching cells using probability topography.""" |
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nuc_mask = (pred_nuc > Config.NUC_THRESHOLD).astype(np.uint8) |
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con_mask = (pred_con > Config.CON_THRESHOLD).astype(np.uint8) |
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markers_raw = np.clip(nuc_mask - con_mask, 0, 1) |
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kernel = np.ones((3,3), np.uint8) |
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markers_clean = cv2.morphologyEx(markers_raw, cv2.MORPH_OPEN, kernel, iterations=1) |
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distance = ndi.distance_transform_edt(markers_clean) |
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coords = peak_local_max(distance, footprint=np.ones((5, 5)), labels=markers_clean, min_distance=5) |
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mask = np.zeros(distance.shape, dtype=bool) |
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mask[tuple(coords.T)] = True |
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markers, _ = ndi.label(mask) |
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return watershed(-distance, markers, mask=nuc_mask) |
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@staticmethod |
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def calculate_morphometrics(label_mask): |
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"""Calculates biological features for each cell.""" |
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regions = regionprops(label_mask) |
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stats = [] |
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for prop in regions: |
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area = prop.area |
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if area < 30: continue |
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perimeter = prop.perimeter |
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if perimeter == 0: continue |
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circularity = (4 * np.pi * area) / (perimeter ** 2) |
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aspect_ratio = prop.major_axis_length / (prop.minor_axis_length + 1e-5) |
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stats.append({ |
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'Area': area, |
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'Perimeter': int(perimeter), |
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'Circularity': round(circularity, 3), |
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'Solidity': round(prop.solidity, 3), |
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'Aspect_Ratio': round(aspect_ratio, 2) |
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}) |
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return pd.DataFrame(stats) |
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@staticmethod |
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def calculate_entropy(prob_map): |
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"""Calculates Shannon Entropy (Uncertainty Map).""" |
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prob_map = np.clip(prob_map, 1e-7, 1-1e-7) |
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entropy = - (prob_map * np.log(prob_map) + (1-prob_map) * np.log(1-prob_map)) |
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return entropy |
