Multiplexed Imaging: CODEX

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/home/administrator/envs/cs-13-dev/lib/python3.13/site-packages/cellSAM/sam_inference.py:351: UserWarning: Low IOU threshold, ignoring mask.
  warnings.warn("Low IOU threshold, ignoring mask.")
/home/administrator/repos/cellSAM/examples/plot_multiplexed.py:17: FutureWarning: `napari.view_image` is deprecated and will be removed in napari 0.7.0.
Use `viewer = napari.Viewer(); viewer.add_image(...)` instead.
  nim = napari.view_image(img, name="CODEX image");

import imageio.v3 as iio
import napari

from cellSAM import cellsam_pipeline
img = iio.imread("../sample_imgs/tissuenet.png")

# Image is 3-channel RGB where Channel 1 (G) represents a nuclear stain
# and Channel 2 (B) a membrane stain. Channel 0 (R) is blank.
print(img.sum(axis=(0, 1)))

mask = cellsam_pipeline(img, use_wsi=False)

nim = napari.view_image(img, name="CODEX image");
nim.add_labels(mask, name="Cellsam segmentation");

if __name__ == "__main__":
    napari.run()