Discuss why we need to close brain regions in Swanson's Brain Maps 4.0. Then give some ideas on how to achive this.

Brain Maps 4.0 is used in many neuroscientific studies to map data onto 2D maps. Among many benefits, mapping the data allows scientists to quantify how the data is distributed across brain regions. The quantification usually involves counts of cells per brain region, for example, or a ranking of fiber density such as low, medium, and high also per brain region. However, there are some brain regions in the atlas that are not fully closed and thus share a continuous space with another brain region. This requires individual labs to draw their own boundaries to determine where to start or stop counting/quantifying. This prohibits reproducibility for some studies unless a lab shares its boundaries with other labs (and the other lab agrees with the boundaries).

A quick note: most of the time these unclosed regions are brain regions regarded as areas, whereas most nuclei with clear Nissl boundaries are represented as fully closed polygons in the Atlas.

From an automation perspective, unclosed regions are also an issue. Instead of manually counting cells or estimating fiber density per brain region, computer programs can be used to automatically quantify these data given all boundaries are closed. Much like the many data maps that showcase demographics, politics, or COVID-19 cases per discrete zip codes, cities, and states, Brain Maps 4.0 needs to be fully defined in order to maximize its use in data analysis.

Part 1

Closing all the brain regions in Brain Maps 4.0 requires experts to come together and propose new boundaries on the existing atlas files. The files are located under the publication's supporting information as "Supporting Information 9". Downloaded folder should be named "SI Folder 2 BM4 Complete Atlas revised".

First, the team would have to manually find the open boundaries and then close them in Adobe Illustrator. To do this, duplicate the atlas and the subdivision color encoding to not alter the original paths, and then set the fill of all duplicated elements as no-fill, and the stroke to solid (no-dash), black, and thin. This will make it easier to identify the gaps in the atlas. Then in a new layer, draw the new boundaries preferably in a different color such as red so they can be easy to identify during the proposal stage.