eTRiP: Easy Tracking Rhythms in Plants

Optimised pipeline to detect periodicity of upwards/downwards movements in plants

This repository contains code for motion detection and modelling based on PyTRiP from github.com/KTgreenham/TRiP. Additionaly a widget has been added to handle the cropping of images.

Installation

The software requires at least Python version 3.12. Optionally you can create and activate a dedicated conda environment for the installation of this software:

conda create -n etrip python=3.12
conda activate etrip

Install from the Python Package Index repository with

pip install --upgrade etrip

Run the imageSelector widget within a jupyter notebook

import etrip

#crop images
etrip.imageSelector("/my/data/directory/original/", "/my/data/directory/cropped/")

Further analysis

#compute motion
etrip.estimateAllMotion("/my/data/directory/cropped/", "/my/data/directory/analysis/")

#fit model
etrip.fitAllMotion("/my/data/directory/analysis/")

Functions

estimateAllMotion( inputDirectory, outputDirectory, ext="jpg" )

Estimate motion for multiple plants

• inputDirectory: directory containing subdirectories for each plant, with each subdirectory containing images for different time points
• outputDirectory: directory where a plant-related subdirectory structure, similar to the inputDirectory, will be created, and where for each plant the detected motion is stored as a CSV file
• ext: extension of the image files to be considered (optional), with a default value of 'jpg'

estimateSingleMotion( inputDirectory, ext="jpg" )

Estimate motion for a single plant. Returns an array containing the estimated motion in both the x and y directions

• inputDirectory: directory containing images of different time points for a single plant
• extension of the image files to be considered (optional), with a default value of 'jpg'

fitAllMotion( analysisDirectory )

Fit model to the motion data

• analysisDirectory: directory containing subdirectories for each plant, with each subdirectory containing motion data as created by the estimateAllMotion function

imageSelector( inputDirectory, outputDirectory, *args, **kwargs)

Tool to create semi-automatically cropped plant images from a series of images of different time points containing multiple plants

• inputDirectory: directory containing multiple plant containing images for different time points
• outputDirectory: directory where a plant-related subdirectory structure is created, where each subdirectory contains the cropped images for the different time points

References

Details of the algorithm, plant imaging set up and examples can be found here: Greenham, K., Lou, P., Remsen, S.E. et al. TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation. Plant Methods 11, 33 (2015). https://doi.org/10.1186/s13007-015-0075-5