ASTEC

This file contains instructions for installing and running the ASTEC reconstruction algorithm. ASTEC is fully described in the following article: Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis

I - CONTENTS OF THE REPOSITORY

Once uncompressed, the folder contains the following elements:

• ASTEC : main source code for the ASTEC package
• LICENCE : the licence terms you accept by using the workflow
• index.ipynb : a notebook example which shows how to run the different functions of the ASTEC segmentation and tracking algorithm
• README.TXT : this file

II - INSTALLATION AND SOFTWARE REQUIREMENTS

ASTEC was fully tested on Unbuntu 14.04 64 bits.

II.i - REQUIREMENTS

In order to be able to compile the different source code you need to install several packages, mostly from the terminal application.

to run the different codes:

• python 2.7 or higher
  • Installation : Should be installed, use the command line python -V to get the installed version or visit https://www.python.org/
• and a c compiler
  • Installation : Should be installed, use the command line dpkg --list | grep compiler to get the list of avaiblable C compiler versions or install gcc with sudo apt-get install gcc

the following libraries are necessary:

• pip, an installer for python (https://pypi.python.org/pypi/pip)
  • Installation : run command line sudo apt-get install python-pip python-dev build-essential
• cmake , a software to build source codes (http://www.cmake.org)
  • Installation : run command line sudo apt-get install cmake

the following libraries are necessary:

• numpy,scipy,matplotlib, different scientific packages for python (http://www.numpy.org, http://www.scipy.org, http://matplotlib.org)
  • Installation : run command line sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
• jupyter notebook, a open-source framework to share scientific code (http://jupyter.org)
  • Installation : run command line sudo pip install jupyter
• zlib, a compression library (http://www.zlib.net) :
  • Installation : run command line sudo apt-get install zlib1g-dev *libhdf5-dev,cython,h5py a library to read/write hdf5 images (https://www.hdfgroup.org/HDF5/)
  • Installation : run command line sudo apt-get install libhdf5-dev, then run sudo pip install cython, then run sudo pip install h5py *pylibtiff, a library to read/write tiff/tif images (https://pypi.python.org/pypi/libtiff/)
  • Installation : run cd path/to/Package/ASTEC/CommunFunctions/libtiff-0.4.0/; sudo python setup.py install

II.ii - INSTALLATION

In order to compile the necessary c folders: in a terminal:

• run cd path/to/Package/ASTEC/CommunFunctions/
• run ./compil.sh

II.iii - TROUBELSHOOTING

The installation of jupyter may failed according of the version of your ipython : to correct this issue run sudo pip install IPython==5.0

III - RUNNING ASTEC

The code of ASTEC, MARS and the FUSION algorithm are written in python and can easly be run with a web interface using a Notebook (http://jupyter.org)

You can find a user interface tutorial here (http://jupyter.cs.brynmawr.edu/hub/dblank/public/Jupyter%20Notebook%20Users%20Manual.ipynb)

To start the notebook, open a terminal and run the command jupyter notebook path/to/Package/index.ipynb