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Working with Image Data

Step 1. Clone the GitHub repository: git clone https://github.com/wolfganghuber/WorkingWithImageData/

Step 2. View a rendered version of the demo at https://www.huber.embl.de/users/whuber/2304-Imaging-Data-in-R/demo.html

Step 3. Follow the steps described in the file demo.qmd in this repository.

To ensure the required R packages are installed, please run BiocManager::install(c("knitr", "dplyr", "ggplot2", "tidyr", "purrr", "devtools", "reshape2", "stringr", "terrainr", "imagefx", "dill/beyonce", "EBImage")).

Make sure your working directory is the top level of the cloned repository. demo.qmd will load example data files (images) from the fig subdirectory of this repository. In addition, it will try to download via the internet some larger files from https://www.huber.embl.de/users/whuber/2304-Imaging-Data-in-R/resources/

Advanced users can try the optional parts of the demo, which involve some longer computations that need the system application (i.e., not R package) ffmpeg installed on your computer. You can obtain it from https://ffmpeg.org or from your package manager. Similarly, youtube-dl from https://youtube-dl.org/ and https://github.com/ytdl-org/youtube-dl/

Further reading: Book chapter in the Modern Statistics for Modern Biology textbook.

This material was first presented on 2023-03-23 in the Workshops for Ukraine series organized by Dariia Mykhailyshyna.

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