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Software is now central to modern transmission electron microscopy. Today’s TEM and STEM workflows depend on automated acquisition, microscope scripting, detector synchronization, tomography reconstruction, 4D-STEM analysis, machine learning, and increasingly autonomous experimental control.
This publication library curates influential papers, software platforms, and research directions that have shaped the software ecosystem for modern electron microscopy.
Software for automated acquisition, targeting, navigation, montaging, and high-throughput TEM workflows.
Tools for diffraction analysis, strain mapping, orientation mapping, ptychography, and pixelated detector data.
Software for tilt-series acquisition, alignment, reconstruction, visualization, and segmentation.
Community-developed tools that support reproducible microscopy data analysis.
Machine learning systems for feature recognition, adaptive acquisition, closed-loop control, and self-driving microscopy.
Software for coordinating microscopes, detectors, sample holders, gas systems, liquid systems, heating, biasing, and experimental metadata.
This review describes software tools used to automate transmission electron microscopy acquisition. It explains how image analysis, microscope control, targeting, navigation, and data handling can be combined into practical automated workflows.
