Metadata-Version: 2.1
Name: colonyscanalyser
Version: 0.3.2
Summary: An image analysis tool for measuring microorganism colony growth
Home-page: https://github.com/Erik-White/ColonyScanalyser/
Author: Erik White
Author-email: 
License: GPL-3.0
Description: [![PyPI version](https://badge.fury.io/py/colonyscanalyser.svg)](https://pypi.org/project/colonyscanalyser/) [![Known Vulnerabilities](https://snyk.io//test/github/Erik-White/ColonyScanalyser/badge.svg?targetFile=requirements.txt)](https://snyk.io//test/github/Erik-White/ColonyScanalyser?targetFile=requirements.txt) [![GitHub](https://img.shields.io/github/license/erik-white/colonyscanalyser?color=blue)](https://github.com/Erik-White/ColonyScanalyser/blob/master/LICENSE)
        
        # ColonyScanalyser
        
        An image analysis tool for measuring microorganism colony growth.
        
        ColonyScanalyser will analyse and collate statistical data from cell-culture plate images. It provides fast, high-throughput image processing.
        
        <img align="right" src="docs/images/growth_curve_small.png">
        
        ColonyScanalyser can provide information on:
        * Colony appearance time
        * Colony growth over time
        * Growth and appearance time distribution (comparing colonies under different conditions)
        
        ColonyScanalyser is suitable for analysing series of images from a fixed point that show the development of microorganism colonies over time.
        
        Several image plots will be output after analysis is complete to enable quick verification of the data. A complete set of data is provided in CSV format for further study.
        
        ## Getting Started
        
        * Install the [prerequisites](#prerequisites) and [package](#installing)
        * Locate your image series in a folder e.g. `/user/images/series1`
        * Run the analysis using ColonyScanalyser
        ```
        scanalyser /user/images/series1
        ```
        
        There are various command line arguments that can alter the way the package is run. To see a list of arguments and information on each, run the command
        ```
        scanalyser --help
        ```
        
        ### Documentation
        A full set of documentation is available at https://erik-white.github.io/ColonyScanalyser/
        
        ### Prerequisites
        
        * [Python](https://www.python.org/) 3.7
        * [Numpy](https://numpy.org/)
        * [Scikit-image](https://scikit-image.org/) >= 0.16
        
        Optionally use a virtual environment, such as [Pipenv](https://github.com/pypa/pipenv).
        
        For testing:
        * [Pytest](https://pytest.org/)
        * [Pytest-cov](https://github.com/pytest-dev/pytest-cov/)
        
        ### Installing
        
        #### Using pip
        ```
        pip install colonyscanalyser
        ```
        
        #### From github (requires [git](https://git-scm.com/) install)
        ```
        git clone https://github.com/erik-white/colonyscanalyser.git
        cd colonyscanalyser
        pip install -e .
        ```
        
        ## Testing
        
        Install the package with the extra test packages:
        `pip install colonyscanalyser[test]`
        
        Run the tests:
        `pytest --cov colonyscanalyser`
        
        ## Contributing
        
        Please read [CONTRIBUTING.md](docs/CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
        
        ## Versioning
        
        We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/erik-white/scanalyser/tags).
        
        ## License
        
        This project is licensed under the GPLv3 - see the [LICENSE](LICENSE) file for details
        
        ## Acknowledgments
        
        * Levin-Reisman et al. for [their work](https://www.ncbi.nlm.nih.gov/pubmed/20676109) developing the ScanLag technique
        * [Fabio Zanini](https://github.com/iosonofabio/) for his original attempts at a Python implementation
        # Changelog
        All notable changes to this project will be documented in this file.
        
        The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
        and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
        
        ## [Unreleased]
        - Full unit test coverage
        - Type annotations on all functions
        
        ## [0.3.2] - 2019-11-11
        - Added documentation
        - Published documentation to GitHub pages (https://erik-white.github.io/ColonyScanalyser/)
        - Add unit tests for the colony module
        
        ## [0.3.1] - 2019-11-04
        ### Fixed
        - Adjust setup to correctly find packages in implicit namespaces
        
        ## [0.3.0] - 2019-11-04
        ### Added
        - Added changelog
        ### Changed
        - Update package to use src structure
        - Update setup for readme compatability with PyPi
        
        ## [0.2.2] - 2019-11-02
        ### Added
        - GitHub action for automatically linting and testing pushes
        - GitHub action for building and releasing package to PyPi
        ### Fixed
        - Linting errors highlighted by flake8
        
        ## [0.2.1] - 2019-10-31
        ### Added
        - Graceful exit if no colonies are found
        - Workaround function to ensure correct plates are found in images
        ### Changed
        - Improve Timepoint grouping by using distance comparison instead of rounding
        - Updated Scikit-image to v0.16
        ### Removed
        - Depreciated Tk import
        - Removed depreciated regionprop coordinates
        
        ## [0.2.0] - 2019-10-28
        ### Added
        - Multiprocessing: greatly improves image processing speed
        - Now shows a progress bar when processing images
        - Snyk security checks for dependencies
        ### Changed
        - Per image processing: now processes a single image at a time
        - Improve colony filtering, removes virtually all merged colonies
        - Updated readme with images and code examples
        ### Fixed
        - Greatly reduced memory usage by using per-image processing
        - Filter out system files when locating images to process
        - Rare divide by zero error when processing colony object data
        
        ## [0.1.2] - 2019-10-13
        Inital release
        ### Added
        - Image processing, plotting and data aggregation
        - Python package uploaded to PyPi
Platform: UNKNOWN
Requires-Python: >=3.7, <3.8
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: dev
