Dataset Information

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.

ABSTRACT:

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).

SUBMITTER: Yuzeir A

PROVIDER: S-EPMC10081871 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Publications

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.

Yuzeir Altay A Bejarano David Alejandro DA Grein Stephan S Hasenauer Jan J Schlitzer Andreas A Yu Jiangyan J

Bioinformatics (Oxford, England) 20230401 4

<h4>Summary</h4>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 a ...[more]

PMID: 36943334

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Dataset Information

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.

Summary

Availability and implementation

Publications

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.

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