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 preexisting 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 (ROIs). 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.

Low intensity repetitive transcranial magnetic stimulation modulates brain-wide functional connectivity to promote anti-correlated c-Fos expression

“…The Ilastik binary object prediction images were further processed using a custom ImageJ plug-in to identify instances of co-expression and output a binary image containing only these c-Fos and parvalbumin co-expressing cells. Finally, both these co-expression images and the Ilastik object prediction images of parvalbumin labelling were mapped to a custom neuroanatomical atlas based on a higher-order region organization of the Allen Mouse Brain Atlas using FASTMAP 68 . This approach facilitated the accurate assessment of the percentage of parvalbumin interneurons which were expressing c-Fos across several higher-order brain regions.…”

Low intensity repetitive transcranial magnetic stimulation modulates brain-wide functional connectivity to promote anti-correlated activity

“…The Ilastik binary object prediction images were further processed using a custom ImageJ plug-in to identify instances of co-expression and output a binary image containing only these c-Fos and parvalbumin co-expressing cells. Finally, both these co-expression images and the Ilastik object prediction images of parvalbumin labelling were mapped to a custom neuroanatomical atlas based on a higher-order region organization of the Allen Mouse Brain Atlas using FASTMAP [37]. This approach facilitated the accurate assessment of the percentage of parvalbumin interneurons which were expressing c-Fos across several higher-order brain regions.…”

Network Neuroscience Untethered: Brain-Wide Immediate Early Gene Expression for the Analysis of Functional Connectivity in Freely Behaving Animals

“…Commercially available tools (e.g., Neu-roInfo [91]) have been developed to facilitate the mapping of labels of interest throughout histological samples. In recent years, open-source atlas registration tools, such as ClearMap, Whole Brain, FASTMAP, DeepSlice, QuickNII, SHARCQ, CUBIC-Cloud, and BrainGlobe, have also emerged as inexpensive and accessible options to further facilitate the registration of biological images to neuroanatomical atlases [92][93][94][95][96][97][98][99] (See Supplemental Table S3 for examples of open-source and commercially available tools for label segmentation and atlas registration).…”