Capillary-based and stokes-based trapping of serial sections for scalable 3D-EM connectomics

Abstract

Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically recon-structed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices, or “sections,” and imaging them, however, handling 10° 106 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e., 102–103 sections. We present a tissue section handling device that transports and positions sections, accurately and repeatability, for automated, robotic section pick-up and placement onto an imaging substrate. The device interfaces with a conventional ultramicrotomy diamond knife, accomplishing in-line, exact-constraint trapping of sections with 100-mm repeatability. An associated mathematical model includes capillary-based and Stokes-based forces, accurately describing observed behavior and fundamentally extends the modeling of water-air interface forces. Using the device, we demonstrate and describe the limits of reliable handling of hundreds of slices onto a variety of electron and light microscopy substrates without significant defects (n =8 datasets composed of 126 serial sections in an automated fashion with an average loss rate and throughput of 0.50% and 63 s/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.