Cell Segmentation for IMC

Cellpose Segmentation

from cellpose import models, io
import numpy as np
import tifffile

# Load image
img = tifffile.imread('processed.tiff')

# Extract nuclear channel (e.g., DNA1)
nuclear_channel = img[0]  # Adjust index based on panel

# Initialize Cellpose model
model = models.Cellpose(model_type='nuclei', gpu=True)