Extracting Timeseries from Images using the xROI R Package

Bijan Seyednasrollah
Table of Contents

In this tutorial, we'll learn how to use an interactive open-source toolkit, the xROI R package that facilitates the process of time series extraction and improves the quality of the final data. The xROI package provides a responsive environment for scientists to interactively:

a) delineate regions of interest (ROIs), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing color-based metrics.

Using the xROI R package, the user can detect FOV shifts with minimal difficulty. The software gives user the opportunity to re-adjust mask files or redraw new ones every time an FOV shift occurs.

xROI Design

The R language and Shiny package were used as the main development tool for xROI, while Markdown, HTML, CSS and JavaScript languages were used to improve the interactivity. While Shiny apps are primarily used for web-based applications to be used online, the package authors used Shiny for its graphical user interface capabilities. In other words, both the User Interface (UI) and server modules are run locally from the same machine and hence no internet connection is required (after installation). The xROI's UI element presents a side-panel for data entry and three main tab-pages, each responsible for a specific task. The server-side element consists of R and bash scripts. Image processing and geospatial features were performed using the Geospatial Data Abstraction Library (GDAL) and the rgdal and raster R packages.

Install xROI

The xROI R package has been published on The Comprehensive R Archive Network (CRAN). The latest tested xROI package can be installed from the CRAN packages repository by running the following command in an R environment.

utils::install.packages('xROI', repos = "http://cran.us.r-project.org" )

Alternatively, the latest beta release of xROI can be directly downloaded and installed from the development GitHub repository.

# install devtools first
utils::install.packages('devtools', repos = "http://cran.us.r-project.org" )

# use devtools to install from GitHub

xROI depends on many R packages including: raster, rgdal, sp, jpeg, tiff, shiny, shinyjs, shinyBS, shinyAce, shinyTime, shinyFiles, shinydashboard, shinythemes, colourpicker, rjson, stringr, data.table, lubridate, plotly, moments, and RCurl. All the required libraries and packages will be automatically installed with installation of xROI. The package offers a fully interactive high-level interface as well as a set of low-level functions for ROI processing.

Launch xROI

A comprehensive user manual for low-level image processing using xROI is available from CRAN xROI.pdf. While the user manual includes a set of examples for each function; here we will learn to use the graphical interactive mode.

Calling the Launch() function, as we'll do below, opens up the interactive mode in your operating system’s default web browser. The landing page offers an example dataset to explore different modules or upload a new dataset of images.

You can launch the interactive mode can be launched from an interactive R environment.

# load xROI

# launch xROI 

Or from the command line (e.g. bash in Linux, Terminal in macOS and Command Prompt in Windows machines) where an R engine is already installed.

Rscript -e “xROI::Launch(Interactive = TRUE)”

End xROI

When you are done with the xROI interface you can close the tab in your browser and end the session in R by using one of the following options

In RStudio: Press the key on your keyboard. In R Terminal: Press on your keyboard.

Use xROI

To get some hands-on experience with xROI, we can analyze images from the dukehw of the PhenoCam network.

You can download the data set from this link (direct download).

Follow the steps below:

First,save and extract (unzip) the file on your computer.

Second, open the data set in xROI by setting the file path to your data

# launch data in ROI
# first edit the path below to the dowloaded directory you just extracted

# alternatively, you can run without specifying a path and use the interface to browse 

Now, draw an ROI and the metadata.

Then, save the metadata and explore its content.

Now we can explore if there is any FOV shift in the dataset using the CLI processer tab.

Finally, we can go to the Time series extraction tab. Extract the time-series. Save the output and explore the dataset in R.

Challenge: Use xROI

Let's use xROI on a little more challenging site with field of view shifts.

Download and extract the data set from this link (direct download, 218 MB) and follow the above steps to extract the time-series.

The xROI R package is developed and maintained by Bijan Seyednarollah. The most recent release is available from https://github.com/bnasr/xROI.

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