Metadata-Version: 2.1
Name: colicoords
Version: 0.1.3
Summary: Create a coordinate system in rod-shaped cells.
Home-page: https://github.com/Jhsmit/ColiCoords
Author: Jochem Smit
Author-email: jhmit@gmail.com
License: MIT
Keywords: cells microscopy ecoli coordinates
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Framework :: Jupyter
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6
Requires-Dist: numpy
Requires-Dist: matplotlib (>=2.2.0)
Requires-Dist: seaborn
Requires-Dist: mahotas
Requires-Dist: multiprocess
Requires-Dist: scipy
Requires-Dist: h5py
Requires-Dist: tifffile
Requires-Dist: tqdm (>=4.27.0)
Requires-Dist: symfit (>=0.4.6)
Requires-Dist: ipywidgets
Requires-Dist: IPython

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|test|

.. |test| image:: images/ColiCoords_Final_Logo.svg
    :width: 50%

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    :target: https://travis-ci.org/Jhsmit/ColiCoords 
.. |appveyor| image:: https://ci.appveyor.com/api/projects/status/801teey9fnm8kuc9?svg=true
    :target: https://ci.appveyor.com/project/Jhsmit/colicoords
.. |docs| image:: https://readthedocs.org/projects/colicoords/badge/?version=latest
    :target: https://colicoords.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
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    :target: https://mybinder.org/v2/gh/Jhsmit/ColiCoords/master
.. |license| image:: https://img.shields.io/badge/License-MIT-yellow.svg
    :target: https://opensource.org/licenses/MIT
.. |doi| image:: https://zenodo.org/badge/92830488.svg
   :target: https://zenodo.org/badge/latestdoi/92830488



Preliminary docs: https://colicoords.readthedocs.io/

Project Goals
=============

ColiCoords is a python project for analysis of fluorescence microscopy data from rodlike cells. The project is aimed to be an open, well documented platform where users can easily share data through compact hdf5 files and analysis pipelines in the form of Jupyter notebooks.


Installation
============

``ColiCoords`` is available on PyPi. To install, python 3.6 is required. A C++ compiler is required for installing the dependency `mahotas  <https://mahotas.readthedocs.io/en/latest/index.html>`_. Alternatively, ``mahotas`` can be install seperately from `Conda <https://conda.io/docs/>`_. 
To install ``ColiCoords`` from pypi:

.. code:: bash

    pip install colicoords


Although `ColiCoords` features automated testing, there are likely to be bugs. Users are encouraged to report them via the Issues page on GitHub. 

Contact: jhsmit@gmail.com

Examples
========

Several examples of `ColiCoords` usage can be found in the examples directory.


|pipeline|

.. |pipeline| image:: images/pipeline_figure.png
    :width: 100%



