Cellpose

CellPose

CellPose is an awesome machine learning-based tool that could segment cells very easily. The pre-trained model could suit multiple scenarios and fit the basic usages. And it can do more than cell segmentation (Though the cell pose looks fancy, I still didn’t know who to work with the results.) To learn more, please read the documentation

from cellpose import models
from cellpose.io import imread

# model_type='cyto' or model_type='nuclei'
model = models.Cellpose(gpu=False, model_type='cyto')

files = ['img0.tif', 'img1.tif']
imgs = [imread(f) for f in files]
masks, flows, styles, diams = model.eval(imgs, diameter=None, channels=[0,1],
                                         flow_threshold=0.4, do_3D=False)