Mouse Connectome: Enhancing the Pipeline for Building a Complete Brain Circuit Map

Abstract

The fundamental mechanisms underlying the operation of the brain remain one of the biggest mysteries in science. The realization of a complete wiring diagram of the mouse hippocampal formation will revolutionize research by enabling detailed investigations into cognitive functions, memory, learning, and neurological disorders. To build a full wiring diagram of the mouse hippocampal formation, 12,000 semithin sections of brain tissue must be cut and collected. The integrity of each section is crucial as the loss of a single section significantly compromises the ability to trace neuronal processes from one section to another. The MagC system, a novel section collection device, offers a promising solution for cutting and collecting these 12,000 sections. However, no established workflow currently exists for utilizing MagC in long-term, large-scale cutting experiments. Specifically, there is no established method to 1) track the number of sections that have been cut, 2) systematically target the sections for detailed imaging, and 3) regularly monitor the sharpness of the knife to determine when a replacement is necessary. This senior capstone project presents an integrated hardware–software system that enhances the workflow of MagC at three critical stages: section counting, section targeting, and knife sharpness monitoring. To this end, a dual-sensor piezoelectric force measurement system was implemented to analyze cutting dynamics, and a machine vision–based software interface was developed for identifying section locations and measuring section compression. The force system enables automatic detection of cutting cycles and provides quantitative metrics—including average force, chatter index, and onset slope—to assess knife condition preemptively. The section targeting interface leverages the Segment Anything Model (SAM) for automated section segmentation and includes manual tools for correction and coordinate export, ensuring all sections can be reliably targeted using electron microscopy. Together, these tools form a robust, scalable MagC workflow for long-term cutting experiments, directly supporting the effort to generate the most comprehensive mouse brain connectome to date.