mousechd-napari.json

{
  "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
}