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Description:

LineageTree 1.4.4

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