Scanning Probe Microscopy: A Comprehensive Guide for Science Students

Scanning probe microscopy (SPM) is a powerful technique in nanometrology, which records sample topography and other physical or chemical surface properties using the forces between a sharp probe and the sample as the feedback source. SPM has an exceptional position in nanometrology due to its simple metrological traceability and minimum sample preparation needs. However, achieving high spatial resolution is demanding, and instruments are prone to systematic errors and imaging artifacts.

Understanding the Principles of Scanning Probe Microscopy

Scanning probe microscopy (SPM) is a family of techniques that utilize a sharp probe to scan the surface of a sample and measure various surface properties, such as topography, electrical, magnetic, and chemical characteristics. The fundamental principle of SPM is the interaction between the probe and the sample surface, which is detected and used as the feedback signal to generate an image.

The main components of an SPM system include:

  1. Probe: A sharp tip, typically made of materials like silicon, silicon nitride, or metal, which interacts with the sample surface.
  2. Piezoelectric Scanner: A device that precisely controls the position of the probe relative to the sample surface, enabling the scanning motion.
  3. Feedback System: A control system that maintains a constant interaction between the probe and the sample surface, such as a constant force or tunneling current.
  4. Detection System: A system that measures the interaction between the probe and the sample, such as deflection of a cantilever or tunneling current.
  5. Data Acquisition and Processing: A system that converts the detected signals into an image or other data representation.

The different SPM techniques, such as Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM), Magnetic Force Microscopy (MFM), and Kelvin Probe Force Microscopy (KPFM), vary in the specific type of probe-sample interaction they utilize and the information they provide about the sample.

Measurement Uncertainty in Scanning Probe Microscopy

scanning probe microscopy

Measurement uncertainty in SPM consists of various sources, including:

  1. Measurements of Known Reference Samples: Calibrating the SPM system using well-characterized reference samples is crucial for accurate measurements. Factors like the quality and traceability of the reference samples can contribute to measurement uncertainty.

  2. Environmental Influences: Factors such as thermal drift, mechanical vibrations, and electrical noise can introduce systematic errors and affect the stability of the SPM system.

  3. Data Processing Impacts: The data processing steps, such as image filtering, background subtraction, and feature extraction, can also introduce uncertainties in the final measurement results.

To analyze and mitigate measurement uncertainty in SPM, researchers often employ modeling and simulation techniques, such as:

  1. Whole Device Level Modeling: Incorporating all instrumentation errors into a large Monte Carlo (MC) model for uncertainty propagation at the whole SPM system level.

  2. Finer Level Modeling: Using ideal, synthesized data to analyze systematic errors related to the measurement principle or typical data processing paths in specific SPM techniques.

The Role of Synthetic Data in Scanning Probe Microscopy

Synthetic data are of increasing importance in nanometrology, with applications in:

  1. Developing Data Processing Methods: Synthetic data can be used to test and validate new data processing algorithms and techniques for SPM, ensuring their robustness and accuracy.

  2. Analyzing Uncertainties: Synthetic data can be used to model the imaging process and data evaluation steps, allowing for a detailed analysis of measurement uncertainties and the identification of systematic errors.

  3. Estimating Measurement Artifacts: Synthetic data can be used to simulate various measurement scenarios, including the presence of known artifacts, to understand their impact on the final measurement results.

Synthetic data can be generated using mathematical models or simulations that accurately represent the physical and chemical processes involved in SPM techniques, such as:

  • Atomic Force Microscopy (AFM): Simulating the interaction between the AFM tip and the sample surface, including van der Waals forces, capillary forces, and electrostatic interactions.
  • Scanning Tunneling Microscopy (STM): Modeling the quantum mechanical tunneling process between the STM tip and the sample surface.
  • Magnetic Force Microscopy (MFM): Simulating the magnetic interactions between the MFM tip and the sample’s magnetic domains.

By using synthetic data, researchers can develop and validate data processing methods, analyze measurement uncertainties, and estimate the impact of various systematic errors and imaging artifacts on the final measurement results.

Comprehensive Software Solutions for Scanning Probe Microscopy

MountainsSPIP® is a dedicated imaging and analysis software for SPM techniques, offering a wide range of tools and functionalities:

  1. Surface Topography Analysis: Detecting and analyzing particles, pores, grains, islands, and other structured surfaces on 3D images.
  2. Spectroscopic Data Correlation: Visualizing, processing, analyzing, and correlating spectroscopic data, such as IR, Raman, TERS, EDS/EDX, and XRF.
  3. Measurement Uncertainty Quantification: Providing tools for estimating and analyzing measurement uncertainties in SPM data.
  4. Synthetic Data Generation: Generating synthetic data to test data processing algorithms and analyze systematic errors.
  5. Advanced Visualization and Reporting: Offering comprehensive visualization and reporting capabilities for SPM data and analysis results.

MountainsSPIP® supports a wide range of SPM techniques, including AFM, STM, MFM, SNOM, CSAFM, and KPFM, making it a versatile and powerful tool for nanometrology and materials characterization.


Scanning probe microscopy is a powerful and versatile technique in nanometrology, with a strong focus on quantifiable data and measurement uncertainty analysis. Synthetic data play a crucial role in understanding and mitigating systematic errors and imaging artifacts, while comprehensive software solutions like MountainsSPIP® provide advanced tools for imaging, analysis, and metrology in SPM techniques. By understanding the principles, measurement uncertainties, and the role of synthetic data, science students can effectively leverage the capabilities of scanning probe microscopy for their research and applications.


  1. Synthetic Data in Quantitative Scanning Probe Microscopy – PMC, 2021-07-02,
  2. MountainsSPIP® image analysis software for scanning probe microscopy techniques including AFM, STM, MFM, SNOM, CSAFM, KPFM – Digital Surf,
  3. Big, Deep, and Smart Data in Scanning Probe Microscopy | ACS Nano, 2016-09-27,
  4. Scanning Probe Microscopy – an overview | ScienceDirect Topics,
  5. Scanning Probe Microscopy – an overview | ScienceDirect Topics,

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