DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection

The precise dissection of anatomically defined brain regions is the basis of many workflows in neurobiology. Traditionally, brain regions of interest are defined by visual inspection of tissue sections, followed by manual dissection. Recently, laser capture microscopes have been employed for more accurate dissection, but region identification is still challenging. This paper presents an open-source software pipeline DART ( D issecting A tlas- R egistered T issue) that aligns histological brain sections to three-dimensional reference atlases and exports the resulting region-of-interest (ROI) contours for dissection by Leica Laser Microdissection (LMD) instruments. By integrating well-established image-processing libraries with a user-friendly graphical user interface, the software automates the traditionally time-consuming workflow of defining the boundaries of brain regions for dissection. With this pipeline, researchers can streamline tissue sampling for molecular analyses, while ensuring reproducibility and precision in ROI selection.