OAT is a python 3 package that allows you to analyze organoids movements and rotation using tracking data.
For the moment, OAT is capable of computing :
- The drift between time points
- The volume for each time points
- The main axis of rotation axis for each time points
- The alignment of the rotation axis with the Z-axis
- The angular velocity for each cell
This package, while able to give some figures of the results, also save all computed data into 2 pandas dataframes for downstream analysis.
The main purpose of this package is to analyze displacement vectors but,
it also gives you to preprocess your 3D data with some tools :
- Filtering of the points for each time points
- Creating a "denoised" stacked timelapse
python 3.8.x
numpy
pandas
scikit-learn
scipy
matplotlib
seaborn
Some jupyter notebooks showing how OAT is used are in /demo.
Visit /method for more informations regarding the methods used :)