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What Electron Microscopy (TEM/SEM) got wrong, from 26 theses
Summary written by a model from the records below: The records describe various experimental and computational failures encountered when applying transmission and scanning electron microscopy to diverse materials and biological specimens. Across these investigations, researchers frequently faced severe difficulties with electron beam damage, specimen preparation artifacts, physical resolution constraints, and digital image processing errors. These records come from graduate theses, 2021 to 2025, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 9 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Electron beam irradiation damages specimens and alters sample properties
Exposure to the electron beam caused polymer degradation, structural collapse of delicate frameworks, defect pinning, and loss of narrow optical emissions. In liquid cells and sensitive compounds, beam radiolysis and interactions triggered bubble formation, uncontrolled precipitation, and unwanted chemical reduction.
Tried and failed
transmission electron microscopy cross-section imaging applied to polymer-supported multilayer thin films. Reason: electron beam damage degraded the polymer substrate during characterization
Investigating photovoltaic performance parameters of organic solar cells under and during 3-point bending flexural testing. · Imperial · PhD
Tried and failed
in situ transmission electron microscopy applied to ionic liquid electrospray emission. Outcome: unstable. Reason: destructive electron beam interactions caused dendritic growth artifacts on the emitting structure
Tried and failed
scanning electron microscopy imaging applied to fluorescent dye-doped organic nanocrystals. Outcome: no signal. Reason: excessive electron beam exposure caused optical damage eliminating narrow molecular emission
Dibenzoterrylene as a single photon source · Imperial · PhD
Tried and failed
scanning electron microscopy imaging applied to organic dye-doped nanocrystals. Outcome: no signal. Reason: electron beam exposure degrades narrow optical emission properties
Towards interfacing single photons emitted from Dibenzoterrylene with rubidium ensemble quantum memories · Imperial · PhD
Tried and failed
time correlation analysis from transmission electron microscopy applied to mesophase orientational relaxation dynamics. Reason: Electron beam exposure introduced defect pinning sites that artificially slowed and distorted the measured relaxation dynamics.
Skyrmion Control and Phase Transitions in Cu2OSeO3 · EPFL · PhD
Tried and failed
transmission electron microscopy with electron diffraction applied to highly oxidizing tetravalent lanthanide compounds. Outcome: unstable. Reason: samples underwent beam-induced reduction in the electron beam
Topology and chemistry of competing interactions in tetravalent lanthanides · Georgia Tech · PhD
Tried and failed
Lorentz transmission electron microscopy magnetic imaging applied to two-dimensional transition metal dichalcogenides. Outcome: no signal. Reason: Electron beam-induced defect generation and charging rapidly degraded magnetic contrast under continuous exposure.
Structural and magnetic characterization of 2D van der Waals materials using scanning transmission electron microscopy · Cornell · PhD
Tried and failed
In situ liquid-cell transmission electron microscopy applied to nanowire electrodes in organic electrolytes. Outcome: unstable. Reason: Electron beam radiolysis caused rapid electrolyte bubbling and uncontrolled nanoparticle precipitation, obscuring observation
In situ electron microscopy of nanomaterials dynamics in heterogeneous phase environments · MIT · PhD
Tried and failed
heavy alkali halide probes in electron microscopy applied to operando liquid-cell STEM imaging. Outcome: unstable. Reason: severe electron-beam-induced damage even at low electron beam doses
OPERANDO METHODS FOR ATOMIC-SCALE MECHANISTIC UNDERSTANDING OF INTERFACIAL ELECTROCATALYSIS · Cornell · PhD
Image processing and reconstruction algorithms fail on noisy or low contrast micrographs
Heuristic thresholding, altered smoothing, and implicit neural representations introduced segmentation artifacts, formed phantom particles, or failed to capture dense microstructures. High spatial heterogeneity, low image contrast, and sample thickness also corrupted automated particle circularity measurements and atomic polarization vector mapping.
Tried and failed
heuristic contrast adjustment and thresholding preprocessing applied to grayscale electron microscopy segmentation. Outcome: worse than baseline. Reason: degraded image quality and disrupted deep learning feature extraction
Deep Learning Approach for Cell Nuclear Pore Detection and Quantification over High Resolution 3D Data · Virginia Tech · Master's
Tried and failed
reducing image smoothing in segmentation pipeline applied to noisy transmission electron microscopy images. Reason: insufficient filtering caused background noise to merge with particles, creating phantom objects and reducing detection accuracy
Standardized Morphology Analysis of Cellulose Nanocrystals via a Semi-Automated Image Processing Approach · Georgia Tech · PhD
Tried and failed
estimating atomic polarization from cation displacement applied to scanning transmission electron microscopy images. Outcome: no signal. Reason: produced noisy, near-centrosymmetric, or reversed-sign vector maps in thick or distorted samples
ATOMIC-SCALE INSIGHTS INTO FERROIC MATERIALS WITH ELECTRON PTYCHOGRAPHY · Cornell · PhD
Instrumental resolution limits and viewing geometry impede nanoscale observation
Scanning electron microscopy techniques lacked sufficient spatial resolution to measure nanoscale precipitates, sub-micron grains, and fine material ripples. In addition, imaging geometries obscured pores behind neighboring cells, while transmission electron microscopy fields of view were too small for representative statistical analysis.
Considered and rejected
Considered and rejected: Transmission electron microscopy (TEM) and optical microscopy (OM) were rejected for quantitative DRX kinetics analysis due to statistically non-representative field of view (TEM) or inability to differentiate LAGBs, HAGBs, and dislocations (OM).
Investigation of microstructural evolution of aluminium alloy 7050 at hot forging conditions · Imperial · PhD
Tried and failed
Scanning electron microscopy applied to nanoscale secondary phase precipitates. Outcome: data insufficient. Reason: Resolution limit was insufficient to resolve and measure nanoscale precipitates.
Ultrasonic characterization of Ti-5Al-5Mo-5V-3Cr · Iowa State · Master's
Considered and rejected
Considered and rejected: Rejected scanning electron microscopy (SEM) due to aerial view obscuring pores behind neighboring endothelial cells/GVs and inability to discern vacuoles from nuclei.
The effect of netarsudil on pore densities of Schlemm's canal inner wall endothelium in human eyes · Boston University · Master's
Tried and failed
scanning electron microscopy with wavelength dispersive spectroscopy applied to sub-micron nanophase metallic grains. Outcome: no signal. Reason: Feature size (~40 nm) was significantly below the instrument spatial resolution limit (~1 µm)
Novel applications of high-resolution environmental and paleomagnetic imaging · Harvard · PhD
Tried and failed
Tilted scanning electron microscopy applied to nanoscale 2D material ripples. Reason: Insufficient resolution for nanometer features and electron beam induced structural relaxation of ripples
Experimental investigations of energy carrier interactions with atomic disorders and artificial long-range orders · UT Austin · PhD
Specimen preparation methods introduce surface damage and drying artifacts
Focused ion beam milling induced surface damage that obscured diffraction contrast, while physical sectioning produced knife marks and specimen folds. Conventional staining and high-vacuum drying procedures caused artificial shrinkage gaps, drying artifacts, and particle agglomeration.
Tried and failed
multibeam transmission electron microscopy imaging applied to focused ion beam prepared specimens. Outcome: no signal. Reason: ion beam preparation induced surface damage artifacts that obscured diffraction contrast features
Microstructural mechanisms of cyclic plasticity and fatigue damage in Ni-based superalloys · Imperial · PhD
Considered and rejected
Considered and rejected: Rejected microscopy images containing knife marks, folds, or prominent visual artifacts from cross-sectional area tracing.
A morphological study on the effect of Thrombospondin-1 on episcleral veins in a TSP-1 deficient mouse model · Boston University · Master's
Considered and rejected
Considered and rejected: Rejected scanning electron microscopy (SEM) in favor of CLSM due to artifact gaps caused by high-vacuum drying and difficulty distinguishing sealer from dentin.
Nachweis der Penetrationstiefe von BioRoot - Sealer in Dentintubuli unter Anwendung verschiedener Obturationsmethoden Demonstration of the penetration depth of BioRoot - Sealer in dentinal tubules using different obturation methods · University of Marburg · PhD
Considered and rejected
Considered and rejected: Rejected conventional transmission electron microscopy (TEM) with negative staining/drying for visualizing MWNT-MS2 heteroaggregates due to drying-induced agglomeration artifacts, utilizing cryo-TEM plunge-freezing instead.
Nanomaterials in complex environments : interactions affected by matrix composition, pH, natural organic matter, and bio- or geo-colloids · UT Austin · PhD
Inelastic scattering, low contrast, and atomic overlap degrade signal quality
Severe inelastic scattering in thick specimens drastically reduced unscattered electron transmission and degraded image signal-to-noise ratios. Similarly, minimal atomic number contrast and overlapping atomic column projections prevented differentiation between chemically identical phases or atomic positions.
Tried and failed
zero-loss energy-filtered transmission electron microscopy applied to thick biological cryo-EM specimens. Outcome: worse than baseline. Reason: Severe inelastic scattering in thick specimens drastically reduced unscattered electron transmission, degrading image SNR
TECHNIQUE ADVANCES AND APPLICATIONS OF CRYO-ELECTRON-MICROSCOPY FOR THE STUDY OF VITRIFIED BIOLOGICAL SYSTEMS · Cornell · PhD
Tried and failed
annular bright-field scanning transmission electron microscopy applied to distinguishing competing crystal structural models. Outcome: no signal. Reason: atomic column projection overlap and low signal-to-noise ratio prevented distinguishing light and heavy atom positions
Quantification of Picometer- to Ångström-Scale Atomic Displacements in Crystals, from Quantum Dots to Bulk Solids · Cornell · PhD
Electrostatic charging and beam-induced heating distort imaging and sample stability
Accumulation of electrostatic charges and local heating induced spurious mechanical deflections and exacerbated specimen degradation at lower acceleration voltages. Furthermore, conductive surface coatings deteriorated under combined thermal cycling and electron beam exposure, resulting in lost imaging resolution.
Tried and failed
lowering acceleration voltage in transmission electron microscopy applied to insulating ceramic specimen imaging. Outcome: worse than baseline. Reason: lower voltage increased sample charging and beam-induced degradation instead of mitigating damage
Tried and failed
scanning electron microscopy for mechanical deflection measurement applied to suspended nanoscale mechanical structures. Outcome: unstable. Reason: electrostatic charging and beam-induced heating caused spurious movement and distorted dynamic measurements
STL NEMS fabrication, design, and inspection · Imperial · PhD
Tried and failed
thin conductive metal coating for in-situ SEM applied to high-temperature electron microscopy imaging. Outcome: unstable. Reason: coating degraded under combined electron beam exposure and thermal cycling, causing severe loss of imaging resolution
Size Effects in Shape Memory Ceramics · MIT · PhD
Left open by the authors
Problems the authors named and did not get to.
Left open
Resolve potential-dependent ionic distribution changes in the electrochemical double layer using operando EC-STEM while mitigating beam damage and concentration issues. Blocker: Requires operando electrochemical scanning transmission electron microscopy (EC-STEM) lab equipment and physical samples
OPERANDO METHODS FOR ATOMIC-SCALE MECHANISTIC UNDERSTANDING OF INTERFACIAL ELECTROCATALYSIS · Cornell · PhD
Left open
Determine whether missing micronuclei in TEM sections of the scuticociliate parasite result from life stage variation or imaging artifacts. Blocker: Requires wet-lab culturing, biological specimens, and transmission electron microscopy (TEM) apparatus.
Left open
Perform cross-sectional transmission electron microscopy of single particle impacts to validate molecular dynamics simulation results. Blocker: Requires specialized physical experimental apparatus and transmission electron microscopy equipment.
Applying molecular dynamics simulations to the study of micro cold spray of yttria · UT Austin · PhD
Left open
Correlate simulated plastic strain gradients with transmission electron microscopy dislocation structures across multiple indentation depths. Blocker: Requires transmission electron microscopy (TEM) experimental facilities and indentation apparatus to observe dislocation structures
Crystal Plasticity Modeling of Heterogeneous Microstructure in Alloys · Georgia Tech · PhD
Left open
Perform transmission electron microscopy analysis to characterize the distribution, evolution, and morphology of oxide film particles near the bonded interface. Blocker: Requires physical bonded aluminum samples and access to transmission electron microscopy (TEM) lab equipment.
Feasibility studies of a novel extrusion-roll-bonding technology · Imperial · PhD
Left open
Investigate electron-beam induced exsolution and re-oxidation reversibility of exsolved nanoparticles on lanthanum nickel oxide double perovskites. Blocker: Requires transmission electron microscopy (TEM) facilities and physical perovskite samples.
Lanthanum nickel oxide based double perovskites and their exsolution phenomena · Imperial · PhD
Left open
Implement TEM-based electron holography or ptychography to image current density at sub-50 nm resolution and correlate flow with defects. Blocker: Requires physical transmission electron microscopy (TEM) experimental apparatus and specialized phase-contrast imaging hardware
Left open
Perform transmission electron microscopy (TEM) nano-characterization to assess crystal defects in AlN/AlGaN/AlN heterostructures. Blocker: Requires physical semiconductor samples and transmission electron microscopy (TEM) lab equipment
Polarization Engineering, Growth and Transport in Next-generation transistors on AlN platform · Cornell · PhD
Left open
Identify the chemical composition and nature of nanometer-scale clusters formed during electron beam damage in AlInN thin films. Blocker: Requires advanced electron microscopy / characterization apparatus (e.g., TEM/EDS/EELS) and physical AlInN samples.
Structural characterization and understanding growth kinetics of modern III-nitride epitaxial methods · Georgia Tech · PhD
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Yao Yang · Cornell · PhD · 2021
OPERANDO METHODS FOR ATOMIC-SCALE MECHANISTIC UNDERSTANDING OF INTERFACIAL ELECTROCATALYSIS - Kunqing Ding · Georgia Tech · PhD · 2026
Crystal Plasticity Modeling of Heterogeneous Microstructure in Alloys - Brayan Vilanova Cuevas · Cornell · PhD · 2025
A MARINE PATHOGENIC PROTIST ACROSS SCALES: HOST-MICROBIOME INTERACTION, PROVENANCE, MORPHOLOGY AND TAXONOMICAL CHARACTERIZATION OF THE SCUTICOCILIATE PARASITE OF DIADEMATIDAE - Harikrishnan Kunhikrishnan Premakumari · Cornell · PhD · 2025
ATOMIC-SCALE INSIGHTS INTO FERROIC MATERIALS WITH ELECTRON PTYCHOGRAPHY - Ariana Ray · Cornell · PhD · 2024
Structural and magnetic characterization of 2D van der Waals materials using scanning transmission electron microscopy - Kimberly Hess · Harvard · PhD · 2024
Novel applications of high-resolution environmental and paleomagnetic imaging - Serin Lee · MIT · PhD · 2024
In situ electron microscopy of nanomaterials dynamics in heterogeneous phase environments - Justin Suh · Boston University · Master's · 2024
A morphological study on the effect of Thrombospondin-1 on episcleral veins in a TSP-1 deficient mouse model - Keisuke Motoki · Georgia Tech · PhD · 2023
Structural characterization and understanding growth kinetics of modern III-nitride epitaxial methods - Jia Guo · Imperial · PhD · 2023
Lanthanum nickel oxide based double perovskites and their exsolution phenomena - Ximo Gallud Cidoncha · MIT · PhD · 2023
Studies on the physical structure, properties and operation of ionic liquid electrosprays in the pure-ion mode - Yue Yu · Cornell · PhD · 2023
TECHNIQUE ADVANCES AND APPLICATIONS OF CRYO-ELECTRON-MICROSCOPY FOR THE STUDY OF VITRIFIED BIOLOGICAL SYSTEMS
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