Quick start guide

Install Python

The most basic requirements for the package are simply Python with its package manager

• Python >= 3.7
• Pip

The installation guide has more information on getting Python.

Install ColonyScanalyser

Once Python is installed the Python package manager, Pip, can be used to install ColonyScanalyser. Open a command line window and install the package:

pip3 install colonyscanalyser

Analyse your images

Now that the ColonyScanalyser package is installed, we can run it from the command line. The package is run with the command scanalyser, followed by any arguments

Try running the command with the --help or -h argument to see a list of available arguments and their default values:

scanalyser --help

The only argument you normally need is the folder path to your images:

scanalyser images_folder/path

If this path contains spaces you must enclose it in quotes:

scanalyser "/images folder/path"

See the command line arguments page for a full list and further details.

If you have entered a correct folder path you will see some messages from ColonyScanalyser as it begins to process and analyse your data.