Installation

Python

ColonyScanalyser requires Python version 3.7 or greater, and the Pip package manager. Pip is included with Python version 3.4 and up.

There are many detailed guides on the web so I will only cover the most basic cases here.

On Mac

The Homebrew package manager is recommended for managing your Python installation.

Once Homebrew is installed, simply open terminal and run the command

brew install python

On Linux

Python may come bundled with your distribution, otherwise it will be available through your package manager e.g.

sudo apt-get install python3.8

On Windows

Go to the Python downloads site and grab the latest Python installer. Run the installer once it has downloaded and follow the setup instructions.

ColonyScanalyser

Use the Python package manager, Pip, to install the ColonyScanalyser package:

pip3 install colonyscanalyser

A message should hopefully indicate that the ColonyScanalyser package was downloaded and installed successfully.

Note: We use the command pip3 in case both Python 2 & 3 are installed on the system. In which case pip will usually default to installing packages for Python 2

If you already have ColonyScanalyser installed via Pip and simply need to update it, use:

pip3 install colonyscanalyser --upgrade

Virtual environments

There are a number of benefits to setting up self-contained virtual environments instead of installing system-wide packages:

• Creates a separate and controlled work environment
• Easily manages complex interdependencies

We use Pipenv which is a combined environment and package manager. Install it with Homebrew:

brew install pipenv

Then create a new Python 3 environment in a workspace folder and install the ColonyScanalyser package:

cd /my/example/workspace
pipenv --three
pipenv install colonyscanalyser

Then run the ColonyScanalyser package:

pipenv run scanalyser /path/to/images

More detailed instructions can be found on the Python packaging site.

Docker

The image is available on Docker Hub.

Alternatively, you can build the image yourself using the Dockerfile included with the package. The container can be built by running docker-build.sh in the scripts directory.

scripts/docker-run.sh is an example of how to use a containerised instance of ColonyScanalyser to analyse images in a directory on the host machine. Run the script as you normally would ColonyScanalyser, passing it the target image directory followed by any other command line arguments:

scripts/docker-run.sh /absolute/path/to/images/ --verbose --plate-size 100