Abstract

Multiple software solutions exist to perform image analysis for object detection, and tools to register 2D slices to 3D reference atlases are also available. The `cuisto` package aims at bridging these pieces of software together to provide a streamlined process, from raw images to quantification figures. It harnesses the output of the bioimage analysis software QuPath used together with the registration toolbox ABBA. Designed with users who have minimal programming knowledge in mind, it is configurable and intended to be atlas- and staining-agnostic to cover various use-cases, and provides utility scripts that can be used throughout the analysis pipeline. Furthermore, extensive documentation is provided, and includes 1) the installation of the various pieces of software used upstream of the `cuisto` package, 2) ABBA and QuPath tutorials, 3) in-depth explanation of the data formatting requirements and 4) hands-on examples with Python scripts and Jupyter notebooks.