Quickstart

Clone the repository and download the pre-trained models:

git clone https://github.com/maxpmx/CelloType.git
cd CelloType

cd models
sh download.sh
cd ..

Prepare the input images

Convert the input images into an RGB format where the blue channel represents the nuclear channel, the green channel corresponds to the membrane channel.

drawing

Inference the cell segmentation

from skimage import io
from cellotype.predict import CelloTypePredictor

img = io.imread('data/example/example_tissuenet.png') # [H, W, 3]

model = CelloTypePredictor(model_path='./models/tissuenet_model_0019999.pth',
  confidence_thresh=0.3,
  max_det=1000,
  device='cuda',
  config_path='./configs/maskdino_R50_bs16_50ep_4s_dowsample1_2048.yaml')

mask = model.predict(img) # [H, W]