2021-03-08

stain tools使用介绍

安装

conda install -c conda-forge python-spams
# 需先安装spams库，windows好像无法安装，只能在linux和maxos上安装
pip install staintools

使用

官方文档

# 读取图片
target = staintools.read_image("目标源图片路径")
to_transform = staintools.read_image("要转换的图片路径")
#即将另外的图片变成target的染色风格

# Standardize brightness (This step is optional but can improve the tissue mask calculation)亮度的标准化
target = staintools.LuminosityStandardizer.standardize(target)
to_transform = staintools.LuminosityStandardizer.standardize(to_transform)

# Stain normalize 
normalizer = staintools.StainNormalizer(method='vahadane')
#method可选择不同的染色归一化方式
normalizer.fit(target)
transformed = normalizer.transform(to_transform)

效果

target_img

to_transform

transformed

stain augmented

# Read data
to_augment = staintools.read_image("./data/my_image_to_augment.png")

# Standardize brightness (This step is optional but can improve the tissue mask calculation)
to_augment = staintools.LuminosityStandardizer.standardize(to_augment)

# Stain augment
augmentor = staintools.StainAugmentor(method='vahadane', sigma1=0.2, sigma2=0.2)
augmentor.fit(to_augment)
augmented_images = []
for _ in range(100):
    augmented_image = augmentor.pop()
    augmented_images.append(augmented_image)