Steps to Run Bilayers Docker Images

1. Pull the Docker Image (CLI or Docker Desktop)¶

Available Docker Images:

• classical_segmentation X Gradio :

  docker pull bilayer/classical_segmentation:1.0.0-gradio

• classical_segmentation X Jupyter_Notebook :

  docker pull bilayer/classical_segmentation:1.0.0-jupyter

• cellpose_inference X Gradio :

  docker pull bilayer/cellpose:1.0.1-gradio

• cellpose_inference X Jupyter_Notebook :

  docker pull bilayer/cellpose:1.0.0-jupyter

• instanseg_inference X Gradio :

  docker pull bilayer/instanseg:1.0.2_pixi_gradio

• instanseg_inference X Jupyter :

  docker pull bilayer/instanseg:1.0.2_pixi_jupyter

Using CLI:

• Open a terminal and run:

docker pull bilayer/<repo_name>:<tag>

Using Docker Desktop (GUI):

• Open Docker Desktop, go to the Images tab, and search for bilayer
• Pull the image directly from DockerHub

2. Run the Docker Container (CLI or Docker Desktop)¶

Using CLI:

• Gradio Interface (No Volume Mount):

docker run -it --rm bilayer/<repo_name>:<tag>

• Jupyter Interface (Requires Volume Mount):

docker run -it --rm -v /path/to/your/data:/bilayers/input_images bilayer/<repo_name>:<tag>

Using Docker Desktop (GUI):

• Gradio: Start the Image as-is, assign it a name, and select an available port (e.g., 8000 for Gradio)

• Jupyter: Use the Volume option to mount your data directory to /bilayers/input_images