Installation

Requirements

We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment. Make sure you are using python 3.

An environment can be created using Anaconda:

$ conda create --name <env>
$ conda activate <env>

Which you can deactivate with:

$ conda deactivate

Or using virtualenv:

$ python -m virtualenv /path/to/venv/
$ source /path/to/venv/bin/activate

This will download all of your packages under /path/to/venv and then activate it. Deactivate using

$ deactivate

You will also need to make sure you have a recent version of pip. In your local environment, run:

$ pip install --upgrade pip

Or using pyenv with pyenv-virtualenv:

$ pyenv install 3.8.14
$ pyenv virtualenv 3.8.14 aliby
$ pyenv local aliby

Pipeline installation

Pip version

Once you have created and activated your virtual environment, run:

If you are analysing data locally:

$ pip install aliby

If you are contacting an OMERO server:

$ pip install aliby[network]

NOTE: Support for OMERO servers in GNU/Linux computers requires building ZeroC-Ice, thus it requires build tools. The versions for Windows and MacOS are provided as Python wheels and thus installation is faster.

Git version

We use poetry for dependency management.

In case you want to have local version:

$ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/aliby.git
$ cd aliby && poetry install --all-extras

This will automatically install the BABY segmentation software. Support for additional segmentation and tracking algorithms is under development.

Troubleshooting

Segmentation has been tested on: Mac OSX Mojave, Ubuntu 20.04 and Arch Linux. Data processing has been tested on all the above and Windows 11.