semvec/pypi-packages huggingface dataset:
colicoords 0.1.5
Create a coordinate system in rod-shaped cells.
License: MIT
Requires Python: >=3.6
Keywords: cells microscopy ecoli coordinates

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`Documentation <https://colicoords.readthedocs.io/>`_

`PLOS One Paper <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217524>`_ 

`BioRxiv Paper <https://www.biorxiv.org/content/10.1101/608109v1>`_

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 and Conda Forge. Currently, python >= 3.6 is required.

Installation by `Conda <https://conda.io/docs/>`_.:

.. code:: bash

     conda install -c conda-forge colicoords 

For installation via PyPi a C++ compiler is required for installing the dependency `mahotas  <https://mahotas.readthedocs.io/en/latest/index.html>`_. Alternatively, ``mahotas`` can be installed separately from Conda. 

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.


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Citation
========

If you you use ``ColiCoords`` for scientific publication, please cite:

Smit, J. H., Li, Y., Warszawik, E. M., Herrmann, A. & Cordes, T. *ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data.* PLOS ONE 14, e0217524 (2019).

If you use the ``CNN`` module please also cite:

Falk, T. et al. *U-Net: deep learning for cell counting, detection, and morphometry.* Nat Methods 16, 67–70 (2019).