An image analysis tool for measuring microorganism colony growth.
ColonyScanalyser will analyse and collate statistical data from cell-culture plate images. It requires a series of images from a fixed point that show the development of microorganism colonies over time.
ColonyScanalyser can provide information on:
- Colony growth lag time (time of appearance)
- Bimodal lag time distribution (comparing lag times of two colonies)
- Colony area growth over time
By default, it will output a set of data and plots that summarize the information from all the plates in the image series. If you require further detail, such as plots of each individual plate, you can increase the save_plots command line argument.
- Install the prerequisites and package
- 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
For example, to run the package 'silently' with no console output: scanalyser \user\images\series1 --verbose 0
- Python >=3.7
- Scikit-image >=0.15
Optionally use a virtual environment, such as Pipenv.
For testing:
Install Scikit-image (unless already installed)
pip install scikit-image
Install ColonyScanalyser
pip install colonyscanalyser
From github (requires git install)
git clone https://github.com/erik-white/colonyscanalyser.git
cd colonyscanalyser
pip install -e .
Install the package with the extra test packages:
pip install colonyscanalyser[test]
Run the tests:
pytest --cov colonyscanalyser
Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.
We use SemVer for versioning. For the versions available, see the tags on this repository.
This project is licensed under the GPLv3 - see the LICENSE file for details
- Levin-Reisman et al. for their work developing the ScanLag technique
- Fabio Zanini for his original attempts at a Python implementation