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
artefacts. We especially focus on substrate preparation, electrostatic effects, and the physical
behavior of sections during transfer and collection. Common artefacts 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.