{ "info": { "author": "Yang Liu, Leon Yang, Curtis Rueden", "author_email": "ctrueden@wisc.edu", "bugtrack_url": null, "classifiers": [], "description": "# Python wrapper for ImageJ\n\n[`imagej.py`](https://github.com/imagej/imagej.py) 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\n default:\n - imglyb\n\nInstall imglyb using `conda install -c hanslovsky imglyb`.\n\nFurther information regarding imglyb can be found in the\n[imglyb GitHub repository](https://github.com/imglib/imglyb).\n\n## Usage\n\nIn this example, replace `/Applications/Fiji.app` with the location of your Fiji installation.\n\n```python\n# Spin up ImageJ.\nimport imagej\nij = imagej.init('/Applications/Fiji.app')\n\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)\nimport imglyb\nij.op().filter().frangiVesselness(imglyb.to_imglib(vessels), imglyb.to_imglib(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\n imagej_server:\n - requests\n - Pillow\n\nUse `pip install -r server_requirements.txt` to install requirements for server.\n\n`Pillow` is required for the imagej.server module's `IJ.show()` function.\nIn addition, `display` or `xv` needs to exist in your system to view the image.\n\n## Usage\n\nThere is a short usage 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