Metadata-Version: 2.3
Name: scopyon
Version: 1.0.0a7
Summary: Monte Carlo simulation toolkit for bioimaging systems
Author: Masaki Watabe, Kazunari Kaizu
Author-email: Masaki Watabe <masaki@riken.jp>, Kazunari Kaizu <kaizu@riken.jp>
License: Copyright (c) 2014, Masaki Watabe
         All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
         
         * Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
         
         * Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
         
         * Neither the name of bioimaging nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
         
         THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
         AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
         IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
         DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
         FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
         DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
         SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
         
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Requires-Dist: hmmlearn>=0.3.3
Requires-Dist: matplotlib>=3.10.8
Requires-Dist: numpy>=2.4.0
Requires-Dist: pint>=0.25.2
Requires-Dist: pyyaml>=6.0.3
Requires-Dist: scipy>=1.16.3
Requires-Python: >=3.13
Project-URL: Documentation, https://scopyon.readthedocs.io/
Project-URL: Repository, https://github.com/ecell/scopyon
Description-Content-Type: text/markdown

scopyon
=======

[![PyPI version](https://badge.fury.io/py/scopyon.svg)](https://badge.fury.io/py/scopyon)
[![Readthedocs](https://readthedocs.org/projects/scopyon/badge/)](http://scopyon.readthedocs.io/)
[![unittest](https://github.com/ecell/scopyon/actions/workflows/unittest.yml/badge.svg)](https://github.com/ecell/scopyon/actions/workflows/unittest.yml)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ecell/scopyon/master)

:microscope: Monte Carlo simulation toolkit for bioimaging systems

Documentation
--------------

See [https://scopyon.readthedocs.io/](https://scopyon.readthedocs.io/) for details.

Requirements
------------

For `scopyon`, Python 3 and its libraries, `numpy`, `scipy`, `matplotlib`, `pyyaml` and `pint`, are required. Installation of `scikit-image`, `pillow` and `plotly` is also recommended.

Installation
------------

```shell-session
$ pip install scopyon
```

or

```shell-session
$ python setup.py test install
```

Quick start
-----------

```shell-session
$ python examples/twocolor.py
```

![TIRF Image](https://github.com/ecell/scopyon/raw/master/examples/twocolor_000.png)

License
-------

`scopyon` is licensed under the terms of BSD-3-Clause (see [LICENSE](/LICENSE)).

Citation
--------

If this package contributes to your work, please cite the followings.

[https://doi.org/10.1371/journal.pone.0130089](https://doi.org/10.1371/journal.pone.0130089)
