Abstract
Background In vitro scratch assays have been widely used to study the influence of bioactive substances on the processes of cell migration and proliferation that are involved in re-epithelialization. The development of high-throughput microscopy and image analysis has enabled scratch assays to become compatible with high-throughput research. However, effective processing and in-depth analysis of such high-throughput image datasets are far from trivial and require integration of multiple image processing and data extraction software tools.FindingsWe developed and implemented a kinetic re-epithelialization analysis pipeline (KREAP) in Galaxy. The KREAP toolbox incorporates freely available image analysis tools and automatically performs image segmentation and feature extraction of each image series, followed by automatic quantification of cells inside and outside the scratched area over time. The enumeration of infiltrating cells over time is modeled to extract three biologically relevant parameters that describe re-epithelialization kinetics. The output of the tools is organized, displayed, and saved in the Galaxy environment for future reference.ConclusionsThe KREAP toolbox in Galaxy provides an open-source, easy-to-use, web-based platform for reproducible image processing and data analysis of high-throughput scratch assays. The KREAP toolbox could assist a broad scientific community in the discovery of compounds that are able to modulate re-epithelialization kinetics.
Highlights
In vitro scratch assays have been widely used to study the influence of bioactive substances on the processes of cell migration and proliferation that are involved in re-epithelialization
The development of high-throughput microscopy and image analysis has enabled scratch assays to become compatible with high-throughput research
We developed and implemented a kinetic re-epithelialization analysis pipeline (KREAP) in Galaxy [17] (Galaxy, RRID:SCR 00628 1) [16] to deliver a web browser-based application for quantitative analysis of in vitro scratch assays based on single-cell recognition
Summary
Cell migration and proliferation play an essential role in a variety of physiological processes, including embryogenesis, angiogenesis, skin and intestinal renewal, and wound repair [1, 2]. Deregulation of these processes can contribute to the development and progression of multiple diseases such as osteoporosis, rheumatoid arthritis, vascular disease, and cancer [1].
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