Analyse timeseries of QFA images

pip install bacolonyzer==2.0.2



Travis (.org) PyPI PyPI - License

by Judith Bergadà Pijuan.

BaColonyzer is a software to quantify the cell density of bacterial cultures from timecourse pictures. It uses image analysis tools to determine the fitness of spotted cultures of bacteria grown on solid agar.


BaColonyzer can be installed under Linux, macOS and Microsoft Windows. It is available in PyPI for Python3.

To install the tool, please run this command in your terminal:

pip3 install bacolonyzer

Further information on the installation can be found in the Installation Guide.


Basic information on how to use BaColonyzer can be obtained using the help flag:

bacolonyzer -h

BaColonyzer has two main commands available for the users. Try the following if you want to get further information:

bacolonyzer analyse -h
bacolonyzer rename_images -h

Alternatively, you can visit the BaColonyzer webpage, where you will find detailed documentation and instructions to use the tool. We highly recommend to visit it in order to understand the input parameters as well as the outputs provided.