{"name":"napari-orientationpy","display_name":"Napari Orientationpy","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-orientationpy.pixels","title":"Orientation measurement","python_name":"napari_orientationpy:OrientationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-orientationpy.distribution","title":"Orientation distribution plot","python_name":"napari_orientationpy:OrientationPlottingWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-orientationpy.pixels","display_name":"Orientation measurement","autogenerate":false},{"command":"napari-orientationpy.distribution","display_name":"Orientation distribution (3D)","autogenerate":false}],"sample_data":[{"key":"bone","display_name":"Bone tissue (2D)","uri":"https://gitlab.com/epfl-center-for-imaging/orientationpy/-/raw/main/data/2D/image1_from_OrientationJ.tif","reader_plugin":null},{"key":"fiber","display_name":"Fibers (3D)","uri":"https://gitlab.com/epfl-center-for-imaging/orientationpy/-/raw/main/data/3D/3dfib.tif","reader_plugin":null}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-orientationpy","version":"0.0.7","dynamic":null,"platform":null,"supported_platform":null,"summary":"Napari plugin for the Orientationpy project.","description":"![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)\n# napari-orientationpy\n\nAnalyze orientations in 2D, 3D, and RGB images in Napari. This plugin is based on the [Orientationpy](https://gitlab.com/epfl-center-for-imaging/orientationpy/) project.\n\n

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\n\n## Installation\n\nYou can install `napari-orientationpy` via [pip]:\n\n pip install napari-orientationpy\n\n## Usage\nTo get started, open an image in the Napari viewer and start `napari-orientationpy` from the `Plugins` menu:\n\n```\nPlugins > Napari Orientationpy > Orientation measurement\n```\n\n1. **Select the structural scale parameter `sigma`**. This value control represents the scale at which the image gradients are computed. Try different values of `sigma` to understand what works best for your images. A reasonable guess would be the order in size, in pixels, of the structures that you are interested in. For example, if you are imaging fibers that appear to be about 4 pixels wide, try to set a value of *sigma=4*.\n\n

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\n\n2. **If you are analyzing a 3D image, select `fiber` or `membrane` mode**. In `fiber` mode, the orientation normals follow fibrous structures. In `membrane` mode, the orientations are normal to the surface of membranous structures.\n\n3. **Decide which outputs you'd like to visualize.**\n - The `color-coded orientation` is a pixel-wise representation of 3D orientations as colors (similar colors = similar orientations).\n - The `orientation vectors` get rendered in a `Vectors` layer in Napari. They are sampled on a regular grid defined by the `Spacing (X)`, `Spacing (Y)` and `Spacing (Z)` values (for 2D images, the `Z` value is ignored). The length of the vectors can be rescaled based on the `energy` value of the orientation computation.\n - You can also output the local `orientation gradient` (misorientation).\n\n4. **Compute orientation**. This button will trigger the orientation computation **only when necessary** (i.e. when the value of `sigma`, the `mode` or the `image` have changed). If you only adjust the `orientation vectors` parameters, clicking the compute button will update the results very fast.\n5. **Save orientation (CSV)**. This will save the orientation measurements as a CSV table with columns `X`, `Y`, `Z`, `theta`, `phi`, `energy`, and `coherency` for all the pixels in the image. \n\n### Plotting the 3D orientation distribution\n\nIf you have computed **orientation vectors** for a 3D image, you can plot their spatial distribution as a `stereographic projection` along the `X`, `Y` or `Z` direction directly in Napari. Select the widget from:\n\n```\nPlugins > Napari Orientationpy > Orientation distribution (3D)\n```\n

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\n\n## Sample images\n\nWe provide a few sample images to test our plugin. Open them from:\n\n```\nFile > Open Sample > Napari Orientationpy\n```\n\n## Contributing\n\nContributions are very welcome. Please get in touch if you'd like to be involved in improving or extending the package.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-orientationpy\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please file an issue along with a detailed description.\n\n----------------------------------\n\n[napari]: https://github.com/napari/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[pip]: https://pypi.org/project/pip/\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/EPFL-Center-for-Imaging/napari-orientationpy.git","download_url":null,"author":"Mallory Wittwer","author_email":"mallory.wittwer@epfl.ch","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","napari[all] >=0.4.16","orientationpy","seaborn","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":null,"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}