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Code for the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level

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Mouse-Atlas

This repository contains the softwares proposed in the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level.

Description of the repository

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.

Basic usage

See the specific README of each folder to have more information.

Dependencies

For each script/class the dependencies are listed in their own README

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Code for the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level

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