Rxiv-Maker: An automated template engine for streamlined scientific publications

Preprints have transformed how biologists share results, yet how well a preprint reads still depends on formatting, a task that has shifted from publishers to authors. Cell biology has also become increasingly quantitative, with conclusions resting on multi-step image analysis whose figures, values, and statistics are revised repeatedly across a project. Keeping a well-formatted manuscript in step with the latest analysis is tedious and error-prone. We introduce Rxiv-Maker, an open-source framework that lets authors write in simple Markdown and produce a formatted article, as a PDF or an editable Word document, with consistent styling, automatic figure and citation numbering, and reliable cross-referencing. For quantitative work, it can optionally regenerate figures and recompute reported values directly from the data, so the text stays consistent with the analysis. Built on familiar tools such as Git and Visual Studio Code, it gives a transparent, collaborative path from analysis to a submission-ready preprint. Researchers have already used Rxiv-Maker for cell-biology studies spanning bacterial cell-cycle analysis, filopodia proteomics, and zebrafish live imaging, showing it supports reproducible reporting of genuine biological findings.