Having your cake and eating it too: Scripted workflows for image manipulation

TL;DR

This paper discusses developing scripted workflows for image manipulation to enhance reproducibility in scientific research, using tools like GIMP and R Shiny to generate active logs of image processing steps.

Contribution

It introduces two approaches—enhancing GIMP and using R Shiny with EBImage—to create reproducible, scriptable image manipulation workflows.

Findings

Active logs successfully replicate image manipulations

Enhanced GIMP produces standalone scripts

R Shiny interface generates reproducible workflows

Abstract

The reproducibility issue in science has come under increased scrutiny. One consistent suggestion lies in the use of scripted methods or workflows for data analysis. Image analysis is one area in science in which little can be done in scripted methods. The SWIIM Project (Scripted Workflows to Improve Image Manipulation) is designed to generate workflows from popular image manipulation tools. In the project, 2 approaches are being taken to construct workflows in the image analysis area. First, the open-source tool GIMP is being enhanced to produce an active log (which can be run on a stand-alone basis to perform the same manipulation). Second, the R system Shiny tool is being used to construct a graphical user interface (GUI) which works with EBImage code to modify images, and to produce an active log which can perform the same operations. This process has been successful to date, but is not complete. The basic method for each component is discussed, and example code is shown.