FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images

Abstract

To better understand complex systems, such as the brain, studying the interactions between multiple brain regions is imperative. Such experiments often require delineation of multiple brain regions on microscopic images based on pre-existing brain atlases. Experiments examining the relationships of multiple regions across the brain have traditionally relied on manual plotting of regions. This process is very intensive and becomes untenable with a large number of regions of interest. To reduce the amount of time required to process multi-region datasets, several tools for atlas registration have been developed; however, these tools are often inflexible to tissue type, only supportive of a limited number of atlases and orientation, require considerable computational expertise, or are only compatible with certain types of microscopy. To address the need for a simple yet extensible atlas registration tool we have developed FASTMAP, a flexible atlas segmentation tool for multi-area processing. We demonstrate its ability to register images efficiently and flexibly to custom mouse brain atlas plates, to detect differences in the regional numbers of labels of interest, and to conduct densitometry analyses. This open-source and user-friendly tool will facilitate the atlas registration of diverse tissue types, unconventional atlas organizations, and a variety of tissue preparations.

SIGNIFICANCE STATEMENT

Wide-scale studies examining relationships between different components of biological systems are becoming increasingly prevalent to diverse scientific questions. This process often requires the registration of biological samples to anatomical atlases. While progress has been made in the development of tools for the registration of mouse and rat brains, these tools are often inflexible to tissue type, tissue preparation, imaging plane, and atlas organization. To answer questions outside of this limited scope, it is imperative that analyses are flexible. To address this need, we have developed an open-source tool to register images to custom atlas plates. This custom registration tool facilitates atlas registration of diverse tissue types, unconventional atlas organizations, and a variety of tissue preparations across many scientific questions.