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 not using an OMERO server setup:

$ pip install aliby

Otherwise, 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.

FAQ¶

Installation fails during zeroc-ice compilation (Windows and MacOS).

For Windows, the simplest way to install it is using conda (or mamba). You can install the (OMERO) network components separately:

$ conda create -n aliby -c conda-forge python=3.8 omero-py
$ conda activate aliby
$ cd c:/Users/Public/Repos/aliby
$ \PATH\TO\POETRY\LOCATION\poetry install

MacOS For local access and processing, follow the same instructions as Linux. Remote access to OMERO servers depends on some issues in one of our depedencies being solved (See issue https://github.com/ome/omero-py/issues/317)

Git version¶

Install poetry for dependency management.

In case you want to have local version:

$ git clone git@gitlab.com/aliby/aliby.git
$ cd aliby

and then either

$$ poetry install --all-extras

for everything, including tools to access OMERO servers, or

$$ poetry install

for a version with only local access, or

$$ poetry install --with dev

to install with compatible versions of the development tools we use, such as black.

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

Omero Server¶

We use (and recommend) OMERO to manage our microscopy database, but ALIBY can process both locally-stored experiments and remote ones hosted on a server.

Setting up a server¶

For testing and development, the easiest way to set up an OMERO server is by using Docker images. The software carpentry and the Open Microscopy Environment, have provided instructions to do this.

The docker-compose.yml file can be used to create an OMERO server with an accompanying PostgreSQL database, and an OMERO web server. It is described in detail here.

Our version of the docker-compose.yml has been adapted from the above to use version 5.6 of OMERO.

To start these containers (in background):

cd pipeline-core
docker-compose up -d

Omit the -d to run in foreground.

To stop them, in the same directory, run:

docker-compose stop

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.

Detailed Windows installation¶

Create environment¶

Open anaconda powershell as administrator

conda create -n devaliby2 -c conda-forge python=3.8 omero-py
conda activate devaliby2

Install poetry¶

You may have to specify the python executable to get this to work :

(Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | C:\Users\USERNAME\Anaconda3\envs\devaliby2\python.exe -

```    Also specify full path when running poetry (there must be a way to sort this)

- Clone the repository (Assuming you have ssh properly set up)
```shell script
git clone git@gitlab.com:aliby/aliby.git
cd aliby
poetry install --all-extras

You may need to run the full poetry path twice - first time gave an error message, worked second time

C:\Users\v1iclar2\AppData\Roaming\Python\Scripts\poetry install --all-extras

confirm installation of aliby - python…import aliby - get no error message

Access the virtual environment from the IDE (e.g., PyCharm)¶

New project In location - navigate to the aliby folder (eg c::/Users/Public/Repos/aliby

Select the correct python interpreter click the interpreter name at the bottom right click add local interpreter on the left click conda environment click the 3 dots to the right of the interpreter path and navigate to the python executable from the environment created above (eg C:\Users\v1iclar2\Anaconda3\envs\devaliby2\python.exe)

Potential Windows issues¶

Sometimes the library pywin32 gives trouble, just install it using pip or conda