Download and Import

Quick installation

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:

cd 'path/to/folder'
pip install .

or for the latest version wihtout cloning the directory

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

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.load('path/to/file.lT')

For ASTEC data:

from lineagetree import read_from_ASTEC
lT = read_from_ASTEC('path/to/ASTEC.pkl')

For MaMuT or TrackMate:

from lineagetree import read_from_mamut_xml
lT = read_from_mamut_xml('path/to/MaMuT.xml')

For TGMM:

from lineagetree import read_from_tgmm_xml
lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)

For Mastodon:

from lineagetree import read_from_mastodon
lT = read_from_mastodon('path/to/Mastodon.mastodon')

or, for Mastodon csv file:

from lineagetree import read_from_mastodon_csv
lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])