ASTEC

This file contains instructions for installing and running the ASTEC reconstruction algorithm.

ASTEC stands for Adaptive Segmentation and Tracking of Embryonic Cells, and was first developed during L. Guignard PhD thesis, Quantitative analysis of animal morphogenesis: from high-throughput laser imaging to 4D virtual embryo in ascidians, Léo Guignard, 2015, https://tel.archives-ouvertes.fr/tel-01278725.

This work was then published on bioRxiv in 2018:

Contact-dependent cell-cell communications drive morphological invariance during ascidian embryogenesis, Léo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, Lars Hufnagel, Grégoire Malandain, Christophe Godin, Patrick Lemaire, bioRxiv 2018; doi: https://doi.org/10.1101/238741.

It was later published in Science in 2020:

Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis, Léo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Julien Laussu, Emmanuel Faure, Gaël Michelin, Kilian Biasuz, Lars Hufnagel, Grégoire Malandain, Christophe Godin, Patrick Lemaire, Science 2020; doi: https://doi.org/10.1126/science.aar5663.

Installation

Only works for Linux or MacOs systems.

I - User installation (without git)

Requires conda.

1. Create a conda environment (here the environment is named astec)

   conda create -n astec -c morpheme -c conda-forge astec

2. Activate the built conda environment

   conda activate astec

Update of packages can be done with

conda update -n astec -c morpheme -c conda-forge astec

II - User installation (with git)

Requires conda and git.

1. Astec code can be found at gitlab.inria.fr/astec/astec. It can be downloaded with

   git clone https://gitlab.inria.fr/astec/astec.git

   It creates an astec directory.

2. Create a conda environment named astec

   cd astec
   conda env create -f pkg/env/astec.yaml

   If already created, the conda environment can be updated with

   conda env update -f pkg/env/astec.yaml

3. Activate the built conda environment

   conda activate astec

III - Developer installation (with git)

Requires conda and git.

1. Astec code can be found at gitlab.inria.fr/astec/astec. It can be downloaded with

   git clone https://gitlab.inria.fr/astec/astec.git

   It creates an astec directory.

2. Create a conda environment named astec-dev

   cd astec
   conda env create -f pkg/env/astec-dev.yaml

   If already created, the conda environment can be updated with

   conda env update -f pkg/env/astec-dev.yaml

3. Activate the built conda environment

   conda activate astec-dev

4. Install astec package for use

   python -m pip install -e .

   The -e option install the package in "editable" mode, this is want you want if you aim at contributing to the astec project. This last command has to be repeated (within the conda environment every time the astec code has been modified).

Tutorial

A tutorial can be found at gitlab.inria.fr/astec/astec-tutorial.

Documentation

A documentation can be found at astec.gitlabpages.inria.fr/astec/.