PT  - JOURNAL ARTICLE
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
TI  - Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics
AID  - 10.1523/ENEURO.0328-19.2019
DP  - 2020 Mar 01
TA  - eneuro
PG  - ENEURO.0328-19.2019
VI  - 7
IP  - 2
4099  - http://www.eneuro.org/content/7/2/ENEURO.0328-19.2019.short
4100  - http://www.eneuro.org/content/7/2/ENEURO.0328-19.2019.full
SO  - eNeuro2020 Mar 01; 7
AB  - 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-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.