In a notebook
See settings for more information on run settings.
import numpy as np import matplotlib.pyplot as plt import skimage.io from cellpose import models # model_type='cyto' or model_type='nuclei' model = models.Cellpose(model_type='cyto') # list of files # PUT PATH TO YOUR FILES HERE! files = ['/media/carsen/DATA1/TIFFS/onechan.tif'] imgs = [skimage.io.imread(f) for f in files] nimg = len(imgs) # define CHANNELS to run segementation on # grayscale=0, R=1, G=2, B=3 # channels = [cytoplasm, nucleus] # if NUCLEUS channel does not exist, set the second channel to 0 channels = [[0,0]] # IF ALL YOUR IMAGES ARE THE SAME TYPE, you can give a list with 2 elements # channels = [0,0] # IF YOU HAVE GRAYSCALE # channels = [2,3] # IF YOU HAVE G=cytoplasm and B=nucleus # channels = [2,1] # IF YOU HAVE G=cytoplasm and R=nucleus # if diameter is set to None, the size of the cells is estimated on a per image basis # you can set the average cell `diameter` in pixels yourself (recommended) # diameter can be a list or a single number for all images masks, flows, styles, diams = model.eval(imgs, diameter=None, channels=channels)
See full notebook at run_cellpose.ipynb.