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Organoid Analyzing Tools (OAT) is a package that allow you to analyze organoids dynamics.

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Organoid Analyzing Tools

Overview

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

Requirements

python 3.8.x
numpy
pandas
scikit-learn
scipy
matplotlib
seaborn

Utilization

Some jupyter notebooks showing how OAT is used are in /demo.
Visit /method for more informations regarding the methods used :)

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Organoid Analyzing Tools (OAT) is a package that allow you to analyze organoids dynamics.

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