The core classes and methods for the python microfluidics, microscopy, data analysis and reporting.
End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines.
### Installation
See [INSTALL.md](./INSTALL.md) for installation instructions.
## Quickstart Documentation
## Quickstart Documentation
We use (and recommend) [OMERO](https://www.openmicroscopy.org/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
### Setting up a server
For testing and development, the easiest way to set up an OMERO server is by
For testing and development, the easiest way to set up an OMERO server is by
using Docker images.
using Docker images.
...
@@ -38,6 +38,10 @@ To stop them, in the same directory, run:
...
@@ -38,6 +38,10 @@ To stop them, in the same directory, run:
docker-compose stop
docker-compose stop
```
```
### Installation
See our [installation instructions](https://aliby.readthedocs.io/en/latest/INSTALL.html) for more details.
We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
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.
Make sure you are using python 3.
An environment can be created with using the conda package manager:
An environment can be created using [Anaconda](https://www.anaconda.com/):
$ conda create --name <env>
$ conda create --name <env>
$ conda activate <env>
$ conda activate <env>
...
@@ -32,33 +30,39 @@ In your local environment, run:
...
@@ -32,33 +30,39 @@ In your local environment, run:
Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
$ pyenv install 3.8.13
$ pyenv install 3.8.14
$ pyenv virtualenv 3.8.13 aliby
$ pyenv virtualenv 3.8.14 aliby
$ pyenv local aliby
$ pyenv local aliby
## Pipeline installation
## Pipeline installation
### Pip version
### Pip version
Once you have created your local environment, run:
Once you have created and activated your virtual environment, run:
If you are analysing data locally:
$ pip install aliby
$ cd aliby
If you are contacting an OMERO server:
$ pip install -e ./
$ 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
### Git version
We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
In case you want to have local version:
In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:
And that should install all three main dependencies in an editable mode. The same process can be used for [BABY](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby)
This will automatically install the [ BABY ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/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.
