Volume Electron Microscopy: Tips & Tricks on Micromanipulator-Assisted Serial Sectioning for Array Tomography

Array tomography (AT), a method in volume electron microscopy (vEM), involves collection of serial ultrathin sections onto substrates for high-resolution imaging and volumetric analysis of biological structures. Success in AT depends on approaches that are precise, reliable, and reproducible. While serial sectioning for AT remains a widely used approach in vEM, details of its practical implementation are often underreported. As a result, critical aspects of serial sectioning, section handling, and collection remain dependent on experience-based knowledge, limiting reproducibility and accessibility. Here, we present a comprehensive, practical guide to serial sectioning using a micromanipulator setup and explain its application in section pickup with various solid substrates, in particular, indium-tin-oxide-coated coverslips. We describe the workflow from block preparation and orientation through trimming, ultramicrotomy, ribbon formation, and section pickup for large datasets, with emphasis on practical decision-making and reducing common artifacts. We especially focus on substrate preparation, electrostatic effects, and the physical behavior of sections during transfer and collection. Common artifacts and errors are examined in the context of upstream process parameters, and strategies to diagnose their root causes are provided. By organizing practical knowledge into a modular framework, this paper aims to improve robustness, reproducibility, and adoption of serial sectioning workflows.