Allen Institute for Brain Science

Senior Software Engineer, Allen Institute for Brain Science — Seattle, 2016–2024.

Over eight years at the Allen Institute, Totte built software for large-scale neuroscience: 3D visualization tools, laboratory automation, and the data pipelines connecting them.

Arboreta — 3D neuron tracing

Arboreta is a desktop application for tracing and reconstructing neurons in three dimensions, built as roughly 100 C++ classes on top of VTK. It ships with an embedded database of around 600 annotated 3D brain regions, letting researchers place each reconstruction in anatomical context as they work.

Laboratory automation

On the Synapse Biology team, Totte developed control software for a six-axis precision robot, coordinating stepper motors, cameras, and a Leica ultramicrotome to automate sample preparation for Array Tomography. He also built an automated GigE video recording system and a barcode-tracked laboratory inventory system backed by MySQL.

Data pipeline

The Array Tomography imaging pipeline combined a PostgreSQL and MySQL backend with a purpose-built front-end UI, giving the lab a single place to track specimens, imaging runs, and results.

Screenshots are not shown here, as this work remains the property of the Allen Institute.