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Yuzeir, A.* ; Bejarano, D.A.* ; Grein, S.* ; Hasenauer, J. ; Schlitzer, A.* ; Yu, J.*

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

Bioinformatics 39:2 (2023)

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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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