Metadata-Version: 2.1
Name: imagej
Version: 0.3.1
Summary: Python wrapper for ImageJ
Home-page: https://github.com/imagej/imagej.py
Author: Yang Liu, Leon Yang, Curtis Rueden
Author-email: ctrueden@wisc.edu
License: Apache 2.0
Description: # Python wrapper for ImageJ
        
        [`imagej.py`](https://github.com/imagej/imagej.py) provides a set of
        wrapper functions for integration between ImageJ and Python.
        
        It also provides a high-level entry point `imagej.IJ` for invoking
        [ImageJ Server](https://github.com/imagej/imagej-server) APIs;
        see "ImageJ Server" below for details.
        
        ## Requirements
        
            default:
            - imglyb
        
        Install imglyb using `conda install -c hanslovsky imglyb`.
        
        Further information regarding imglyb can be found in the
        [imglyb GitHub repository](https://github.com/imglib/imglyb).
        
        ## Usage
        
        In this example, replace `/Applications/Fiji.app` with the location of your Fiji installation.
        
        ```python
        # Spin up ImageJ.
        import imagej
        ij = imagej.init('/Applications/Fiji.app')
        
        # Import an image with scikit-image.
        import skimage
        from skimage import io
        # NB: Blood vessel image from: https://www.fi.edu/heart/blood-vessels
        img = io.imread('https://www.fi.edu/sites/fi.live.franklinds.webair.com/files/styles/featured_large/public/General_EduRes_Heart_BloodVessels_0.jpg')
        import numpy as np
        img = np.mean(img, axis=2)
        
        # Invoke ImageJ's Frangi vesselness op.
        vessels = np.zeros(img.shape, dtype=img.dtype)
        import imglyb
        ij.op().filter().frangiVesselness(imglyb.to_imglib(vessels), imglyb.to_imglib(img), [1, 1], 20)
        ```
        
        See also `test/test_imagej.py` for other examples of usage.
        
        
        # ImageJ Server
        
        ## Requirements
        
            imagej_server:
            - requests
            - Pillow
        
        Use `pip install -r server_requirements.txt` to install requirements for server.
        
        `Pillow` is required for the imagej.server module's `IJ.show()` function.
        In addition, `display` or `xv` needs to exist in your system to view the image.
        
        ## Usage
        
        There is a short usage example
        [here](https://github.com/imagej/imagej.py/blob/master/imagej/server/usage.py).
        
Platform: any
Description-Content-Type: text/markdown
