TY - JOUR T1 - Capillary- and Stokes-based trapping of serial sections for scalable 3D-EM connectomics JF - eneuro JO - eNeuro DO - 10.1523/ENEURO.0328-19.2019 SP - ENEURO.0328-19.2019 AU - Timothy J. Lee AU - Mighten C. Yip AU - Aditi Kumar AU - Colby F. Lewallen AU - Daniel J. Bumbarger AU - R. Clay Reid AU - Craig R. Forest Y1 - 2020/02/24 UR - http://www.eneuro.org/content/early/2020/02/24/ENEURO.0328-19.2019.abstract N2 - Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed 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 µm repeatability. An associated mathematical model includes capillary- 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 seconds/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.Significance Statement Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for studying neuroanatomy. However, between the process of cutting the slices and imaging them, handling 10°-106 delicate slices—or “sections”—remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e.,102-103 sections. Here, we present a section handling device that transports and positions sections for automated, robotic section pick-up and placement onto an imaging substrate. As a part of this device, we characterize a trapping technique that utilizes curvature-induced capillary-based forces and hydrodynamic Stokes drag-based forces. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics. ER -