{"name":"mousechd-napari","display_name":"MouseCHD","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"mousechd-napari.get_reader","title":"Open data with MouseCHD","python_name":"mousechd_napari._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"mousechd-napari.widget","title":"Create MouseCHD widget","python_name":"mousechd_napari._widget:MouseCHD","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"mousechd-napari.sample","title":"sample","python_name":"mousechd_napari.sample_data:load_sample","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"mousechd-napari.get_reader","filename_patterns":["*.nrrd","*.nii.gz","*.dcm"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"mousechd-napari.widget","display_name":"MouseCHD","autogenerate":false}],"sample_data":[{"command":"mousechd-napari.sample","key":"sample","display_name":"micro-CT scan"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"mousechd-napari","version":"0.0.4","dynamic":null,"platform":null,"supported_platform":null,"summary":"A tool for heart segmentation and congenital heart defect detection in mice.","description":"# Napari plugin for MouseCHD project\n\n![](https://raw.githubusercontent.com/hnguyentt/mousechd-napari/master/assets/demo.gif)\n\n*Tool for heart segmentation and congenital heart defect detection in mice.*\n\n## Installation\n\nThere are several ways to run the plugin: (1) from bundle, (2) Containers (Docker or Apptainer), (3) from code\n\n### From Bundle\n\n(1) Install Napari by following this instruction https://napari.org/stable/tutorials/fundamentals/installation.html#install-as-a-bundled-app\n\n(2) Install `mousechd-napari` plugin:\n    * Run Napari\n    * `Plugins` --> `Install/Uninstall Plugins ...` --> Search for `mousechd-napari` --> Click on `install`.\n\n(3) Restart Napari to run the plugin\n\n\n### Containers\n#### Docker\n##### Pull docker\n```\nsudo docker pull hoanguyen93/mousechd-napari\n```\n\n##### Run MouseCHD Plugin\n* Run plugin with local resources:\n\n    ```\n    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\n    ```\n\n    <details>\n    <summary>Example:</summary>\n\n    ```\n    sudo docker run --gpus all -v /home/hnguyent:/home/hnguyent -it --rm -p 9876:9876 -p 6006:6006 hoanguyen93/mousechd-napari\n    ```\n\n    </details>\n\n    Open this link on your browser: [http://localhost:9876/](http://localhost:9876/)\n\n* Run plugin with server resources:\n\n    * Follow [this instruction](./docs/server_setup.md) to setup running on server.\n    * Copy ~/.ssh folder to a temporary location, for example in ~/Downloads: `cp -r ~/.ssh ~/Downloads/`\n    * Change ownership for temporary ~/Downloads/.ssh folder: `chown -R root:root ~/Downloads/.ssh`\n    * 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`\n    * Open this link on your browser: [http://localhost:9876/](http://localhost:9876/)\n\n##### Known issues\n* The plugin in docker container can't display 3D view, please choose 2D view to display the sample and images.\n\n#### Apptainer (Singularity)\nIf you want to run with server resource, follow [this instruction](./docs/server_setup.md) to setup running on server.\n\n* 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`\n* Run the plugin: \n```\napptainer exec \\\n    --nv \\\n    --bind /tmp/.X11-unix:/tmp/.X11-unix \\\n    --env DISPLAY=$DISPLAY \\\n    <path/to/mousechd-napari.sif> napari\n```\n\n### From code\n\n```bash\nconda create -n mousechd_napari python=3.9\nconda activate mousechd_napari\npip install \"napari[all]\"\npip install mousechd-napari\nnapari\n```\n\n## How to use\nPlease find details instruction in folder [docs](https://github.com/hnguyentt/mousechd-napari/tree/master/docs)\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/hnguyentt/mousechd-napari","download_url":null,"author":"Hoa Nguyen","author_email":"ntthoa.uphcm@gmail.com","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["setuptools","packaging","mousechd","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/hnguyentt/mousechd-napari/issues","Documentation, https://github.com/hnguyentt/mousechd-napari#README.md","Source Code, https://github.com/hnguyentt/mousechd-napari","User Support, https://github.com/hnguyentt/mousechd-napari/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}