lineagetree 3.2.0

Structure for Lineage Trees

LineageTree

Documentation available at LineageTree Documentation

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 Amat 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
• Data from the Digital development Database described in Du et al. 2014 and Du et al. 2015
• and few others

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'])

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