Metadata-Version: 1.1
Name: small-particle-detection
Version: 0.0.3
Summary: Small Particle Detection, a shapes library-based object detector.
Home-page: https://gitlab.inria.fr/ncedilni/spade
Author: Nicolas Cedilnik
Author-email: nicolas.cedilnik@inria.fr
License: CeCILL
Description: SPADE: Small PArticle DEtection
        ===============================
        
        .. image:: http://www-sop.inria.fr/morpheme/images/logo2.png
           :width: 200 px
           :target: http://www-sop.inria.fr/morpheme/team.html
        
        An algorithm primarily design to detect objects whose sizes aren't larger a
        few pixels (particles) on fluorescence microscopy images.
        
        It is an simplified version of marked point process.
        
        
        Requirements
        ============
        SPADE has only been tested with Python 3.5 but should work with older versions.
        The only strict requirement is the package `numpy`.
        In order to use SPADE to its full extent, we recommend installing the
        `scikit-image` package and the full `scipy` ecosystem.
        
        
        Usage
        =====
        
        In a python script
        ------------------
        
        You can install the package using PIP. The main function, `spade2d`, is in the
        `spade.detection_2d` module. It takes an image, a shapes library and a
        threshold as input. A typical usage would look like like
        
        .. code:: python
        
            from skimage.io import imread, imshow
            from skimage.filters import threshold_otsu
            from skimage.color import label2rgb
            from numpy import percentile
            import matplotlib.pyplot as plt
        
            from spade.detection_2d import spade2d
            from spade.shapes.examples import potatoids5x5_smallest4px
        
        
            # Load the example image.
            image = imread("example_2d.png")
        
            # Separate cell image from background, using by Otsu's thresholding method.
            cell = image > threshold_otsu(image)
        
            # Focus on brightest pixels only
            potential_centers = image > percentile(image[cell], 99)
        
            # Detect particles.
            particles = spade2d(image=image,
                                shapes_library=potatoids5x5_smallest4px,
                                threshold=20,
                                potential_centers=potential_centers,
                                mask=cell)
        
            # Show detected particles as overlay on our original image.
            imshow(label2rgb(particles, image, bg_label=0))
            plt.show()
        
        
        See the examples in the `example` folder of the source dist for more
        information. Note that `matplotlib` and `skimage` are not required for SPADE
        to work.
        
        From the command line
        ---------------------
        
        Also provided is a command line interface, that can be used as following:
        
        .. code:: bash
        
            python -m spade.cli INPUT_IMAGE THRESHOLD -o /path/to/output_image.png
        
        Launch this command with `-h` for more information on its usage.
        
        
        
        Authors & Acknowledgments
        =========================
        
        
        SPADE was developed by `Nicolas Cedilnik
        <mailto:nicoco@nicoco.fr>`_, `Éric Debreuve
        <http://www.i3s.unice.fr/~debreuve/>`_ and `Xavier Descombes
        <http://www-sop.inria.fr/members/Xavier.Descombes/>`_ at the `MORPHEME team
        <http://www-sop.inria.fr/morpheme/team.html>`_.
        
        If you use SPADE for your scientific work, please include this `bibtex` (or
        equivalent) entry:
        
        .. code:: latex
        
            @misc{cedilnik2016spade,
              title={SPADE: Small particle detection}
              author={Cedilnik, Nicolas and Debreuve, Éric and Descombes, Xavier}
              url={https://pypi.python.org/pypi/small-particle-detection}
              year={2016}
            }
        
        License
        =======
        SPADE is released under the `CeCILL-2.1 licence
        <http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.txt>`_.
        
Keywords: image,image processing,scientific research
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Classifier: License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)
Classifier: Programming Language :: Python :: 3.5
