MouseCHD

Tool for heart segmentation and congenital heart defect detection in mice.

Installation¶

There are several ways to run the plugin: (1) from bundle, (2) Containers (Docker or Apptainer), (3) from code

From Bundle¶

(1) Install Napari by following this instruction https://napari.org/stable/tutorials/fundamentals/installation.html#install-as-a-bundled-app

(2) Install mousechd-napari plugin: * Run Napari * Plugins --> Install/Uninstall Plugins ... --> Search for mousechd-napari --> Click on install.

(3) Restart Napari to run the plugin

Containers¶

Docker¶

Pull docker¶

sudo docker pull hoanguyen93/mousechd-napari

Run MouseCHD Plugin¶

• Run plugin with local resources:

  sudo docker run --gpus all -v <path/to/home/on/host>:<path/to/home/on/host> -it --rm -p 9876:9876 -p 6006:6006 hoanguyen93/mousechd-napari

  Example:

  sudo docker run --gpus all -v /home/hnguyent:/home/hnguyent -it --rm -p 9876:9876 -p 6006:6006 hoanguyen93/mousechd-napari

  Open this link on your browser: http://localhost:9876/

• Run plugin with server resources:

  • Follow this instruction to setup running on server.
  • Copy ~/.ssh folder to a temporary location, for example in ~/Downloads: cp -r ~/.ssh ~/Downloads/
  • Change ownership for temporary ~/Downloads/.ssh folder: chown -R root:root ~/Downloads/.ssh
  • Run docker: udo docker run --gpus all -v <path/to/home/on/host>:<path/to/home/on/host> -v /home/hnguyent/Downloads/.ssh:/root/.ssh:ro -it --rm -p 9876:9876 -p 6006:6006 hoanguyen93/mousechd-napari
  • Open this link on your browser: http://localhost:9876/

Known issues¶

• The plugin in docker container can't display 3D view, please choose 2D view to display the sample and images.

Apptainer (Singularity)¶

If you want to run with server resource, follow this instruction to setup running on server.

• Download Apptainer image mousechd-napari.sif from (Zenodo)[https://zenodo.org/records/14652180] or simply: wget https://zenodo.org/records/14652180/files/mousechd-napari.sif
• Run the plugin:

apptainer exec \
    --nv \
    --bind /tmp/.X11-unix:/tmp/.X11-unix \
    --env DISPLAY=$DISPLAY \
    <path/to/mousechd-napari.sif> napari

From code¶

conda create -n mousechd_napari python=3.9
conda activate mousechd_napari
pip install "napari[all]"
pip install mousechd-napari
napari

How to use¶

Please find details instruction in folder docs