TY - JOUR T1 - GIANI: open-source software for automated analysis of 3D microscopy images JF - bioRxiv DO - 10.1101/2020.10.15.340810 SP - 2020.10.15.340810 AU - David J. Barry AU - Claudia Gerri AU - Donald M. Bell AU - Rocco D’Antuono AU - Kathy K. Niakan Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/10/16/2020.10.15.340810.abstract N2 - The study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a lack of user-friendly, open-source software to analyse such images. Here we describe GIANI (djpbarry.github.io/Giani), new software for the analysis of 3D images, implemented as a plugin for the popular FIJI platform. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images and also comes with scripting and command line tools, such that users can incorporate its functionality into their own scripts and easily run GIANI on a high-performance computing cluster. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in mouse early embryos. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.Competing Interest StatementThe authors have declared no competing interest. ER -