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IntestLine: A shiny-based application to map the rolled intestinal tissue onto a line.
Bioinformatics 39:2 (2023)
SUMMARY: To allow the comprehensive histological analysis of the whole intestine, it is often rolled to a spiral before imaging. This Swiss-rolling technique facilitates robust experimental procedures, but it limits the possibilities to comprehend changes along the intestine. Here, we present IntestLine, a Shiny-based open-source application for processing imaging data of (rolled) intestinal tissues and subsequent mapping onto a line. The visualization of the mapped data facilitates the assessment of the whole intestine in both proximal-distal and serosa-luminal axis, and enables the observation of location-specific cell types and markers. Accordingly, IntestLine can serve as a tool to characterize the intestine in multi-modal imaging studies. AVAILABILITY AND IMPLEMENTATION: Source code can be found at Zenodo (https://doi.org/10.5281/zenodo.7081864) and GitHub (https://github.com/SchlitzerLab/IntestLine).
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Publication type
Article: Journal article
Document type
Scientific Article
ISSN (print) / ISBN
1367-4803
Journal
Bioinformatics
Quellenangaben
Volume: 39,
Issue: 4,
Article Number: 2
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)
Grants
EXC Hausdorff Center for Mathematics
Emmy Noether Research Grant
EXC Immuno Sensation 2
German Research Foundation
Emmy Noether Research Grant
EXC Immuno Sensation 2
German Research Foundation