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        "author": "Curtis Rueden, Leon Yang, Yang Liu, Michael Pinkert",
        "author_email": "ctrueden@wisc.edu",
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        "description": "# Python wrapper for ImageJ\n\n[`pyimagej`](https://github.com/imagej/pyimagej) provides a set of\nwrapper functions for integration between ImageJ and Python.\n\nIt also provides a high-level entry point `imagej.IJ` for invoking\n[ImageJ Server](https://github.com/imagej/imagej-server) APIs;\nsee \"ImageJ Server\" below for details.\n\n## Requirements\n\nInstall dependencies using `conda env create -f environment.yml`.\n\nSee also:\n\n* [scyjava](https://github.com/scijava/scyjava)\n* [imglyb](https://github.com/imglib/imglyb)\n\n## Usage\n\n### Creating the ImageJ gateway\n\n#### Newest available version\n\nIf you want to launch the newest available release version of ImageJ:\n\n```python\nimport imagej\nij = imagej.init()\n```\n\nThis invocation will automatically download and cache the newest release of\n[net.imagej:imagej](http://maven.imagej.net/#nexus-search;gav~net.imagej~imagej~~~).\n\n#### With graphical capabilities\n\nIf you want to have support for the graphical user interface:\n\n```python\nimport imagej\nij = imagej.init(headless=False)\nij.ui().showUI()\n```\n\nNote there are issues with Java AWT via Python on macOS; see\n[this article](https://github.com/imglib/imglyb#awt-through-pyjnius-on-osx)\nfor a workaround.\n\n#### Including ImageJ 1.x support\n\nBy default, the ImageJ gateway will not include the\n[legacy layer](https://imagej.net/Legacy) for backwards compatibility with\n[ImageJ 1.x](https://imagej.net/ImageJ1).\nYou can enable the legacy layer as follows:\n\n```python\nimport imagej\nij = imagej.init('net.imagej:imagej+net.imagej:imagej-legacy')\n```\n\n#### Including Fiji plugins\n\nBy default, the ImageJ gateway will include base ImageJ2 functionality only,\nwithout additional plugins such as those that ship with the\n[Fiji](https://fiji.sc/) distribution of ImageJ.\n\nYou can create an ImageJ gateway including Fiji plugins as follows:\n\n```python\nimport imagej\nij = imagej.init('sc.fiji:fiji')\n```\n\n#### From a local installation\n\nIf you have an installation of [ImageJ2](https://imagej.net/ImageJ2)\nsuch as [Fiji](https://fiji.sc/), you can wrap an ImageJ gateway around it:\n\n```python\nimport imagej\nij = imagej.init('/Applications/Fiji.app')\n```\n\nReplace `/Applications/Fiji.app` with the actual location of your installation.\n\n### Using the ImageJ gateway\n\nOnce you have your ImageJ gateway, you can start using it. Here is an example:\n\n```python\n# Import an image with scikit-image.\nimport skimage\nfrom skimage import io\n# NB: Blood vessel image from: https://www.fi.edu/heart/blood-vessels\nimg = io.imread('https://www.fi.edu/sites/fi.live.franklinds.webair.com/files/styles/featured_large/public/General_EduRes_Heart_BloodVessels_0.jpg')\nimport numpy as np\nimg = np.mean(img, axis=2)\n\n# Invoke ImageJ's Frangi vesselness op.\nvessels = np.zeros(img.shape, dtype=img.dtype)\nij.op().filter().frangiVesselness(ij.py.to_java(vessels), ij.py.to_java(img), [1, 1], 20)\n```\n\nSee also `test/test_imagej.py` for other examples of usage.\n\n\n# ImageJ Server\n\n## Requirements\n\nThe imagej.server module has its own requirements:\n\n* `requests` is required to communicate with the ImageJ server.\n* `pillow` is required for the `imagej.server.IJ.show()` function.\n  In addition, `display` or `xv` must be available to view the image.\n\n## Usage\n\nThere is a short usage example\n[here](https://github.com/imagej/imagej.py/blob/master/imagej/server/usage.py).\n\n\n",
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