Welsh Mouse Embryo Stager

Stage a mouse embryo in the age range E14 -> E15 by drawing a spline on a photographic image.

Install and run

• Install miniconda (if needed) from here.

• Install vedo and scipy by typing:

pip install vedo -U
conda install scipy

• Copy the repository locally

git clone https://github.com/marcomusy/welsh_embryo_stager.git
cd welsh_embryo_stager

• Run the program, eg.:

python stager.py pics/E14.5_L3-03_HL2.5X.jpg

• Draw a spline by clicking points on your image

• Can also read and stage a text file directly with, eg.:

python stager.py pics/E14.5_L3-03_HL2.5X_LHL.txt

5. Press q when finished, an output window will show up with the age of the embryo

The above output image and a text file with clicked points are saved to directory output/ for reference.

Description

Use three shape descriptors to calibrate the age over a dataset of about 190 embryos. The algorithm gives reliable estimates only in the range E14 to E15, outside of this range results are not reliable. User should check that finger peaks and valleys (marked in green and red) on the left plot are reasonably well identified.

The error estimation is completely heuristic and should be taken as a rough indication, the red sphere represents the uncertainty in the parameter space. You can interact with the 3D scene of the bottom-right plot.

To generate a standalone executable

With pyinstaller do:

rm build dist __pycache__
pyinstaller stager.spec

This will create a dist/stager.exe file, which you can test with e.g.:

dist/stager.exe pics/E14.5_L3-03_HL2.5X.jpg