LMDmapper: an open-source desktop tool for spatial mapping of laser microdissection samples

Laser microdissection (LMD) enables researchers to isolate targeted microsamples from microscopy slide specimens for downstream molecular analyses. While traditionally employed for isolating eukaryotic cells from complex tissues, LMD is starting to be used for micro-scale spatial microbiome analyses, which require the precise location of the microsamples to be tracked for downstream spatial analyses. To address this need, we present LMDmapper, an open-source desktop application that allows designing, tracking and logging micron-scale spatial microsample data and metadata from LMD sessions. The software parses Leica Database LIF image files (containing stage coordinates), imports laser microdissection CSV exports (containing image pixel coordinates), transforms and maps image pixel coordinates into stage coordinates, and presents the resulting cut points together with user-defined plate layouts and collection metadata. LMDmapper supports a variety of microdissection designs, including multiple slides, specimens, collection plates and plate layouts. The application is implemented in TypeScript using Electron, React, Vite, and fast-xml-parser. LMDmapper outputs include a metadata CSV linking microsample identifiers to plate positions, collection information, image labels, pixel coordinates and stage coordinates, as well as the possibility to create overview images of the specimens, and automatically calculating distances between cutting points and regions of interest. With these capabilities, LMDmapper is intended as a practical bridge between microscope-side laser microdissection records and downstream spatial omics sample tracking.