LineageTree

This library allows to import and work with cell (but not limited to cells) lineage trees. With LineageTree you can read from:

• TGMM algorithm outputs described in Fernando et al. 2014
• TrackMate files described in Tinevez et al. 2017
• MaMuT files described in Wolff et al. 2018
• SVF algorithm outputs described in McDole, Guignard et al. 2018
• ASTEC algorithm outputs described in Guignard, Fiuza et al. 2020
• and few others

Description of the repository

• src: folder containing the package
• setup.py: Installation script
• README.md: This file
• LICENCE: The licence describing file

Basic usage

Once installed the library can be called the following way (as an example):

from LineageTree import lineageTree

and one can then load lineage trees the following way:

For .lT files:

lT = lineageTree('path/to/file.lT')

For ASTEC data:

lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')

or

lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')

For SVF:

lT = lineageTree('path/to/SVF.bin')

For MaMuT:

lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')

For TrackMate:

lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')

For TGMM:

lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')

For Mastodon:

lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')

or, for Mastodon csv file:

lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')

Dependencies

Some dependecies are requiered:

• general python dependecies:
  • numpy, scipy
• specific dependency:
  • svgwrite if svg output is needed

Quick install

To quickly install the library together with its dependencies one can run:

pip install LineageTree

or, for the latest version if you have cloned the directory:

pip install .

or for the latest version wihtout cloning the directory

pip install git+https://github.com/leoguignard/LineageTree