Brodmann Explorer

Multiscale brain modeling environment bridging anatomy, function, and simulation

Brodmann Explorer was my first serious attempt at building neuroscience software.

The original idea was large. Probably too large. I wanted to create an interactive environment for exploring the brain across scales: gross anatomy, cortical regions, functional circuits, time-series activity, and eventually simulation. In my head, it was somewhere between a brain atlas, a modeling workspace, a research notebook, and an extensible analysis tool.

That is a lot... for a while, I pushed it hard anyway.

The project went through multiple versions, starting with early PySide6 interface experiments and growing into a more complete desktop prototype with 3D visualization, network views, plugin systems, time synchronization, synthetic EEG visualization, and reproducible pipeline concepts. I explored architecture for custom objects, tool configurations, and analysis pipelines, including early file formats for saving structured tool states and chaining workflows together.

Ultimately, this gave me a stronger understanding of the biotech software ecosystem, the limitations of current tools and infrastructure, and the foundation for what I continue to study and work on in my free time. Though Brodmann Explorer has been deprioritized, I continue to develop it slowly as I gain more software development ability and neuroscience expertise.

Project Media

Update 11/05/2025

Brodmann Explorer V9 can now support visualization and reproducible analysis end to end. The priority now is to sharpen purpose and build some set of specific tools, moving from “looks cool” to “does useful work.” After attending an Allen Institute workshop held at Western Washington University, I’m evaluating their workflows and tools against my focus areas to determine which processes I can build to support analysis of AIND data...

Update 08/10/2025

Brodmann Explorer v8 is now fully functional and hitting our original goals. The object, tool/plugin, pipeline architecture is stable, with .iltaobj and .iltapip fully implemented to capture tool configurations and chain them into reproducible pipelines. Global time sync works smoothly across views. EEG visualization is in and will keep improving with tuning. Themes are live... Stark looks pretty cool.

Project Details

Role: Architect, developer, designer
Built with: PySide6, PyVista, NetworkX, Figma, yEd
Scope: Neuroscience visualization, modeling, plugin architecture, prototype analysis workflows
Status: In Progress

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