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"description": "[](https://pypi.org/project/colonyscanalyser/) [](https://snyk.io//test/github/Erik-White/ColonyScanalyser?targetFile=requirements.txt) [](https://github.com/Erik-White/ColonyScanalyser/blob/master/LICENSE)\n\n# ColonyScanalyser\n\nAn image analysis tool for measuring microorganism colony growth.\n\nColonyScanalyser will analyse and collate statistical data from agar plate images. It provides fast, high-throughput image processing.\n\n![](\"docs/images/growth_curve_linear_small.png\")
\n\nColonyScanalyser can provide information on:\n* Colony appearance time\n* Growth parameters (lag time, rate, carrying capacity)\n* Growth and appearance time distribution\n* Colony colour (e.g. staining or other visual indicators)\n\nColonyScanalyser is suitable for analysing series of images from a fixed point that show the development of microorganism colonies over time.\n\nSeveral 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.\n\n## Getting Started\n\n* Install the [prerequisites](#prerequisites) and [package](#installing)\n* Locate your image series in a folder e.g. `/user/images/series1`\n* Run the analysis using ColonyScanalyser\n```\nscanalyser /user/images/series1\n```\n\nThere 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\n```\nscanalyser --help\n```\n\n### Documentation\nA full set of documentation is available at https://erik-white.github.io/ColonyScanalyser/\n\n### Prerequisites\nColonyScanalyser requires Python version 3.7 or greater, and the Pip package manager. Pip is included with Python version 3.4 and up.\n\nThe remaining Python package dependencies are automatically handled by Pip when installing the Colonyscanalyser package.\n\n![](\"docs/images/plate_map_small.png\")
\n\nOptionally use a virtual environment, such as [Pipenv](https://github.com/pypa/pipenv), or a [containerised instance of the package](https://hub.docker.com/r/erikwhite/colonyscanalyser).\n\nFor testing:\n* [Pytest](https://pytest.org/)\n* [Pytest-cov](https://github.com/pytest-dev/pytest-cov/)\n\n### Installing\n\n#### Using pip\n```\npip install colonyscanalyser\n```\n\n#### From github (requires [git](https://git-scm.com/) install)\n```\ngit clone https://github.com/erik-white/colonyscanalyser.git\ncd colonyscanalyser\npip install -e .\n```\n\n## Testing\n\nInstall the package with the extra test packages:\n`pip install colonyscanalyser[test]`\n\nRun the tests:\n`pytest --cov colonyscanalyser`\n\n## Contributing\n\nPlease read the [contribution guidelines](docs/CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.\n\n## Versioning\n\nWe use [SemVer](http://semver.org/) for versioning. For the versions available, see the [releases](https://github.com/Erik-White/ColonyScanalyser/releases).\n\n## License\n\nThis project is licensed under the GPLv3 - see the [licence](LICENSE) file for details\n\n## Acknowledgments\n\n* Levin-Reisman et al. for [their work](https://www.ncbi.nlm.nih.gov/pubmed/20676109) developing the ScanLag technique\n* [Fabio Zanini](https://github.com/iosonofabio/) for his original attempts at a Python implementation\n# Changelog\nAll notable changes to this project will be documented in this file.\n\nThe format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),\nand this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).\n\n## [0.6.2] - 2021-01-25\n### Added\n- Savitzky\u2013Golay filtering for curve fitting and plotting\n### Fixed\n- Removed leftover debugging message\n\n## [0.6.0] - 2021-01-24\n### Added\n- An `align` subpackage containing image alignment functionality\n- Image alignment verification and correction before processing images\n- Command line arguments to adjust image alignment strategy and tolerance\n### Changed\n- Growth curves now use a windowed median which should help to smooth the curve\n### Fixed\n- Various warnings emitted when running the tests\n\n## [0.5.3] - 2020-09-07\n### Changed\n- Updated and improved IdentifiedCollection, now backed by a Dictionary for easier lookup\n### Fixed\n- Images are now correctly converted when creating image animations, fixing buffer errors\n\n## [0.5.2] - 2020-07-05\n### Changed\n- Removes the temporary fix used when identifying plate centres\n\n## [0.5.1] - 2020-06-07\n### Fixed\n- RGB images are correctly handled during colour mode conversion\n\n## [0.5.0] - 2020-06-05\n### Added\n- Utilize multiprocessing for grouping and filtering `Timepoint`s to Colonies\n- `silent` command line argument to prevent output to console\n- `animation` command line argument to output\n- New class function, from_path, for building an ImageFileCollection\n### Changed\n- Improved plot labels/legends\n- `plots` command line argument replaced with `no-plots` switch\n- `multiprocessing` command line argument replaced with `single-process` switch\n- Reworked command line arguments, using simplified switches for boolean arguments\n- Reworked command line arguments to follow GNU conventions\n- Refactored `main` module\n- Improve access model and remove forward typing\n### Fixed\n- Ensure image files are converted to RGB\n\n## [0.4.4] - 2020-06-03\n### Fixed\n- Plots are now saved to the correct directory again\n\n## [0.4.3] - 2020-06-02\n### Added\n- `--version` command line argument to display installed package version number\n- `--image_formats` command line argument to display supported image formats\n- Package configuration and now consolidated and loaded from a settings module\n### Changed\n- Improved the output from the `--help` command line argument to make it a little clearer\n\n## [0.4.2] - 2020-05-18\n### Added\n- Support for `bmp` image files\n### Fixed\n- Wrong type reference in colony.colonies_from_timepoints\n### Changed\n- `image_file._load_image` will now retry once if it fails\n## [0.4.1] - 2020-05-11\n### Added\n- Dockerfile and utility scripts\n- Docker image is now available: https://hub.docker.com/r/erikwhite/colonyscanalyser\n## [0.4.0] - 2020-03-26\n### Added\n- `plate_labels` command line argument\n- `base` module with base classes to provide core functionality throughout the package\n- `geometry` module with base shape classes\n- `plate` module with `Plate` and `PlateCollection` classes\n- `image_file` module with `ImageFile` and `ImageFileCollection` classes\n- `growth_curve` module to provide curve fitting and parameters\n- `plot_plate_images_animation` outputs animated gifs for each plate in two sizes\n- Output a summary of plate properties to `plates_summary.csv`\n- Full type hinting for all modules\n### Changed\n- Extended compatibility to Python 3.8\n- Cached data is now not used by default\n- Individual plots for each plate are now output by default\n- `use_saved` command line argument renamed to `use_cached_data`\n- Compressed serialised data filename changed to `cached_data`\n- `save_plots` command line argument renamed to `plots`\n- `plate_size` now defaults to 90 mm, the visible size of a 100 mm plate in a plate holder\n- `plate_edge_cut` is now a percentage of the plate diameter, instead of a fixed pixel value\n- Refactored most of the functions from `main` as static methods in the `plate` or `image_file` modules\n- Improved flexibility when detecting date and time stamp information in file names\n- Replaced growth properties in `Colony`, now implemented as `growth_curve.GrowthCurveModel`\n- Modified plots to use new `GrowthCurveModel` properties\n- Improved colony segmentation in low contrast images and under poor growth conditions\n- Grouping of colony Timepoints is now faster and more accurate\n- Colonies are no longer identified based on circularity\n### Fixed\n- A rare error when opening images using skimage.io.imread\n- Corrected default DPI settings and conversion factor\n### Removed\n- A number of Colony properties - now implemented by `growth_curve.GrowthCurveModel`\n\n## [0.3.4] - 2020-01-18\n### Added\n- plate_edge_cut command line argument\n- Plate and colony ID map to show how they have been identified\n### Changed\n- Add border exclusion and slightly relax colony circularity filtering in segment_image\n\n## [0.3.3] - 2019-12-19\n### Added\n- Colony colour identification and grouping\n- Webcolors package and rgb_to_name function to provide CSS colour groupings\n### Fixed\n- crop_image will now correctly handle images without an alpha channel\n\n## [0.3.2] - 2019-11-11\n### Added\n- Documentation\n- Published documentation to GitHub pages (https://erik-white.github.io/ColonyScanalyser/)\n- Unit tests for the colony module\n\n## [0.3.1] - 2019-11-04\n### Fixed\n- Adjust setup to correctly find packages in implicit namespaces\n\n## [0.3.0] - 2019-11-04\n### Added\n- Added changelog\n### Changed\n- Update package to use src structure\n- Update setup for readme compatability with PyPi\n\n## [0.2.2] - 2019-11-02\n### Added\n- GitHub action for automatically linting and testing pushes\n- GitHub action for building and releasing package to PyPi\n### Fixed\n- Linting errors highlighted by flake8\n\n## [0.2.1] - 2019-10-31\n### Added\n- Graceful exit if no colonies are found\n- Workaround function to ensure correct plates are found in images\n### Changed\n- Improve Timepoint grouping by using distance comparison instead of rounding\n- Updated Scikit-image to v0.16\n### Removed\n- Depreciated Tk import\n- Removed depreciated regionprop coordinates\n\n## [0.2.0] - 2019-10-28\n### Added\n- Multiprocessing: greatly improves image processing speed\n- Now shows a progress bar when processing images\n- Snyk security checks for dependencies\n### Changed\n- Per image processing: now processes a single image at a time\n- Improve colony filtering, removes virtually all merged colonies\n- Updated readme with images and code examples\n### Fixed\n- Greatly reduced memory usage by using per-image processing\n- Filter out system files when locating images to process\n- Rare divide by zero error when processing colony object data\n\n## [0.1.2] - 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