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

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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.\nAVAILABILITY AND IMPLEMENTATION: Source code can be found at Zenodo (https://doi.org/10.5281/zenodo.7081864) and GitHub (https://github.com/SchlitzerLab/IntestLine).", "claims": [{"id": "claim-data-access", "statement": "Supplementary data is available at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36943334", "locator": "sections[12] \"Supplementary data\" paragraph 2", "quote": "Supplementary data is available at Bioinformatics online."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36943334"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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