Bell Jar: A Semi-Automated Registration and Cell Counting Tool for Mouse Neurohistology Analysis
Engineering
Koret Scholarship
In this paper, I introduce Bell Jar, a multi-platform tool that aids users in aligning their tissue to a reference atlas and can perform cell detection and quantification. The problem of aligning and registering reference atlases to neurohistology data has been a critical effort in contemporary neuroinformatics. The ability to accurately register experimental tissue to an atlas enables automated determination of experimental cells areas and layers for rapid quantification of experiments. Despite widespread efforts to solve this problem, most available tools are paid products or complicated compilations of scripts tuned for only one kind of data. Bell Jar provides these tools in one easy-to-navigate application that manages its dependencies, supports various data types, and requires no programming expertise.
