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
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'])
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