Metadata-Version: 2.1
Name: stardist
Version: 0.2.1
Summary: StarDist
Home-page: https://github.com/mpicbg-csbd/stardist
Author: Uwe Schmidt, Martin Weigert
Author-email: uschmidt@mpi-cbg.de, mweigert@mpi-cbg.de
License: BSD 3-Clause License
Description: # StarDist
        
        ![](https://github.com/mpicbg-csbd/stardist/raw/master/images/overview.png)
        
        
        The code in this repository implements object detection with star-convex polygons as described in the paper:
        
        Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers.  
        [*Cell Detection with Star-convex Polygons*](https://arxiv.org/abs/1806.03535).  
        International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018.
        
        Please cite the paper if you are using this code in your research.
        
        
        
        ``` 
        @inproceedings{schmidt2018,
          author    = {Uwe Schmidt and Martin Weigert and Coleman Broaddus and Gene Myers},
          title     = {Cell Detection with Star-Convex Polygons},
          booktitle = {Medical Image Computing and Computer Assisted Intervention - {MICCAI} 
          2018 - 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part {II}},
          pages     = {265--273},
          year      = {2018},
          doi       = {10.1007/978-3-030-00934-2\_30},
        }
        ```
        
        
        
        
        ## Installation
        
        This package requires Python 3.5 (or newer) and can be installed with `pip`:
        
            pip install stardist
        
        ### Notes
        
        - Depending on your Python installation, you may need to use `pip3` instead of `pip`.
        - Since this package relies on a C++ extension, you could run into compilation problems (see [Troubleshooting](#troubleshooting) below). We currently do not provide pre-compiled binaries.
        - StarDist uses the deep learning library [Keras](https://keras.io), which requires a suitable [backend](https://keras.io/backend/#keras-backends) (we only tested [TensorFlow](http://www.tensorflow.org/)).
        
        
        ## Usage
        
        We provide several Jupyter [notebooks](https://github.com/mpicbg-csbd/stardist/tree/master/examples) that illustrate how this package can be used.
        
        ![](https://github.com/mpicbg-csbd/stardist/raw/master/images/example_steps.png)
        
        
        ## Troubleshooting
        
        Installation requires Python 3.5 (or newer) and a working C++ compiler. We have only tested [GCC](http://gcc.gnu.org) (macOS, Linux), [Clang](https://clang.llvm.org) (macOS), and [Visual Studio](https://visualstudio.microsoft.com) (Windows 10). Please [open an issue](https://github.com/mpicbg-csbd/stardist/issues) if you have problems that are not resolved by the information below.
        
        If available, the C++ code will make use of [OpenMP](https://en.wikipedia.org/wiki/OpenMP) to exploit multiple CPU cores for substantially reduced runtime on modern CPUs. This can be important to prevent the function `star_dist` ([utils.py](https://github.com/mpicbg-csbd/stardist/blob/master/stardist/utils.py)) from slowing down model training.
        
        
        ### macOS
        Although Apple provides the Clang C/C++ compiler via [Xcode](https://developer.apple.com/xcode/), it does not come with OpenMP support.
        Hence, we suggest to install the OpenMP-enabled GCC compiler, e.g. via [Homebrew](https://brew.sh) with `brew install gcc`. After that, you can install the package like this (adjust names/paths as necessary):
        
            CC=/usr/local/bin/gcc-8 CXX=/usr/local/bin/g++-8 pip install stardist
        
        
        ### Windows
        Please install the [Build Tools for Visual Studio 2017](https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2017) from Microsoft to compile extensions for Python 3.5 and 3.6 (see [this](https://wiki.python.org/moin/WindowsCompilers) for further information). During installation, make sure to select the *Visual C++ build tools*. Note that the compiler comes with OpenMP support.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.5
Description-Content-Type: text/markdown
