This repository contains TARDIS the software that coregister embryos, proposed in the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level
Folders:
- Annotation-example: Example of annotations for TARDIS. The xml files are MaMuT xml files (https://imagej.net/MaMuT).
- csv-parameter-files: Example of parameterization csv files for TARDIS.
Python files:
- TARDIS.py: python script to coregister two segmented embryos.
The TARDIS.py python script proposed here can be run from a terminal the following way:
python TARDIS.py
It is then prompted to provide a parameter csv file (example provided in the folder csv-parameter-files). The path to the parameter file should be then typed in the terminal.
If the package have been installed using setup.py, the script can be call just by typing TARDIS.py from anywhere in the terminal
Some dependecies are requiered:
- general python dependecies:
- numpy, scipy, pandas
- TARDIS.py:
- TGMMlibraries has to be installed (https://github.com/leoguignard/TGMMlibraries)
- Transformations has to be installed (https://github.com/leoguignard/Transformations)
To quickly install the script so it can be call from the terminal and install too the common dependecies one can run
python setup.py install [--user]Still will be remaining to install Transformations and TGMMlibraries packages.