Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 539663
Title KREAP : An automated Galaxy platform to quantify in vitro re-epithelialization kinetics
Author(s) Fernandez-Gutierrez, Marcela M.; Zessen, David B.H. van; Baarlen, Peter van; Kleerebezem, Michiel; Stubbs, Andrew P.
Source GigaScience 7 (2018)7. - ISSN 2047-217X
DOI https://doi.org/10.1093/gigascience/giy078
Department(s) Host Microbe Interactomics
VLAG
WIAS
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) Cell migration - Galaxy - High-throughput - Image analysis - Modeling - Re-epithelialization - Scratch assay - Workflow - Wound healing
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. Findings: We 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. Conclusions: The 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.

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