This repository contains the softwares proposed in the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level.
For each of the folders, you can refer to their specific helps. Folders:
- IO: The class
SpatialImage, a container for images and input/output. When the right external libraries are installed (see in the so called folder), can read tiff, hdf5, klb and inr images. - TGMMlibraries: The class
lineageTree, a container for lineage trees and Statistical Vector Flow (SVF). Can read output data from TGMM or MaMuT. - Transformation: A class for linear transformations manipulation writen by Christoph Gohlke from Laboratory for Fluorescence Dynamics in University of California (http://www.lfd.uci.edu/~gohlke/).
- SVF: The scripts SVF-prop.py and tissue-bw-prop.py
- TARDIS: The script TARDIS.py
- Time-registration: The standalone-registration.py
- I2AE: The script that allows to register an intensity image onto our average embryo
- svf2MaMuT: The script that allows to write an SVF output onto a MaMuT interpretable xml file.
See the specific README of each folder to have more information.
For each script/class the dependencies are listed in their own README