Metadata-Version: 2.1
Name: colonyscanalyser
Version: 0.3.4
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 agar 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
        * Colony colour (e.g. staining or other visual indicators)
        
        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
        ColonyScanalyser requires Python version 3.7, and the Pip package manager. Pip is included with Python version 3.4 and up.
        
        The remaining Python package dependencies are automatically handled by Pip when installing the Colonyscanalyser package.
        
        <img align="right" src="docs/images/plate_map_small.png">
        
        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
        
        ## [0.3.4] - 2020-01-18
        ### Added
        - plate_edge_cut command line argument
        - Plate and colony ID map to show how they have been identified
        ### Changed
        - Add border exclusion and slightly relax colony circularity filtering in segment_image
        
        ## [0.3.3] - 2019-12-19
        ### Added
        - Colony colour identification and grouping
        - Webcolors package and rgb_to_name function to provide CSS colour groupings
        ### Fixed
        - crop_image will now correctly handle images without an alpha channel
        
        ## [0.3.2] - 2019-11-11
        ### Added
        - Documentation
        - Published documentation to GitHub pages (https://erik-white.github.io/ColonyScanalyser/)
        - 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: dev
Provides-Extra: test
