Skip to main content

Create a coordinate system in rod-shaped cells.

Project description

travis appveyor Documentation Status binder codecov license doi

test

Documentation

PLOS One Paper

BioRxiv Paper

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.:

conda install -c conda-forge colicoords

For installation via PyPi a C++ compiler is required for installing the dependency mahotas. Alternatively, mahotas can be installed separately from Conda.

To install ColiCoords from pypi:

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

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).

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for colicoords, version 0.1.5
Filename, size File type Python version Upload date Hashes
Filename, size colicoords-0.1.5-py2.py3-none-any.whl (81.1 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size colicoords-0.1.5.tar.gz (53.3 MB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page