Second Harmonic Generation Microscopy

Second Harmonic Generation Microscopy

Microscopy has been an indispensable tool in scientific research for centuries, enabling the observation and analysis of structures beyond the limits of human vision. Second Harmonic Generation Microscopy (SHGM) is a relatively modern technique that harnesses the unique nonlinear optical properties of materials to provide high-resolution imaging. This article by Academic Block aims to provide a comprehensive overview of SHGM, starting with the fundamental principles underlying its functionality.

Principles of Second Harmonic Generation

SHG microscopy relies on the nonlinear optical process of second harmonic generation, where two incident photons combine to produce a photon with twice the frequency and half the wavelength. This phenomenon is particularly useful in imaging biological tissues, as certain structures, such as collagen fibers, exhibit strong SHG signals.

Understanding the principles of SHG microscopy requires a grasp of the underlying physics. SHG occurs when a nonlinear material, such as biological tissues, is illuminated by an intense laser beam. The incident photons interact with the nonlinear medium, causing electrons to undergo a coherent, nonlinear response that results in the emission of second harmonic photons.

In biological tissues, collagen is a major contributor to SHG signals due to its non-centrosymmetric structure. Collagen fibers, a crucial component of the extracellular matrix, generate strong SHG signals, allowing researchers to visualize and study these structures without the need for exogenous labels.

The polarization dependence of SHG provides additional contrast, enabling the differentiation of different tissue components. By manipulating the polarization of the incident light, researchers can selectively enhance or diminish SHG signals from specific structures, offering a versatile tool for imaging various biological specimens.

Applications of SHG Microscopy

SHG microscopy has found diverse applications in the study of biological tissues and materials. One prominent area of application is in the field of connective tissue research. Collagen, a primary structural protein in connective tissues, plays a crucial role in maintaining tissue integrity. SHG microscopy allows researchers to visualize collagen fibers in three dimensions, providing insights into tissue organization, remodeling, and diseases such as fibrosis.

Moreover, SHG microscopy has been extensively used in neuroscience to study myelinated fibers and axonal structures. The non-invasive nature of SHG imaging makes it ideal for observing live samples, enabling longitudinal studies of dynamic processes within neural tissues.

In cancer research, SHG microscopy has shown promise in characterizing the collagen organization within tumors. Changes in collagen architecture are often associated with tumor progression, invasion, and metastasis. SHG imaging can aid in identifying these alterations, offering potential diagnostic and prognostic information.

Mathematical equations behind the Second Harmonic Generation Microscopy

The mathematical equations behind Second Harmonic Generation (SHG) microscopy involve principles from nonlinear optics and can be quite complex. The key equation that governs the generation of the second harmonic signal is based on the nonlinear polarization induced in a material by the incident laser field. Here are the fundamental equations:

Nonlinear Polarization:

The nonlinear polarization, P(2ω), induced in a material due to the second harmonic generation can be expressed as:

P(2ω)(t) = ϵ0 χ(2) E(ω)(t) E(ω)(t) ;


      • P(2ω) is the induced polarization at the second harmonic frequency (),
      • ϵ0 is the vacuum permittivity,
      • χ(2) is the second-order nonlinear susceptibility,
      • E(ω)(t) is the electric field of the incident laser beam at the fundamental frequency ω

Electric Field at the Second Harmonic:

The electric field at the second harmonic, E(2ω)(t), can be obtained by solving the wave equation:

2 E(2ω) − [ (1 / c2) ( ∂2 E(2ω) / ∂t2 ) = (−1 / ϵ0 c2) (∂2P(2ω) / ∂t2) ;

Here, c is the speed of light.

Simplifying the Equations:

In the case of SHG microscopy, it is common to use a monochromatic incident field, and under certain approximations, the equations can be simplified. Assuming a plane wave for the incident field, E(ω)(t) = E0 ei(kz−ωt) ; where E0 is the amplitude and k is the wave vector, the equations can be further simplified.

With these assumptions, the electric field at the second harmonic becomes:

E(2ω)(t) = [ (1 / 2) χ(2) (E0)2 ei(2kz − 2ωt) ] ;

Intensity at the Second Harmonic:

The intensity at the second harmonic is proportional to the square of the electric field. The detected signal in SHG microscopy, I(2ω), is often given as:

I(2ω) ∝ ∣E(2ω) (t)∣2 ;

Substituting the expression for E(2ω)(t), this becomes:

I(2ω) ∝ ∣χ(2)2 ∣E04 ;

This equation highlights the quadratic dependence of the second harmonic intensity on the incident field.

These equations provide the foundation for understanding the principles of Second Harmonic Generation Microscopy. The specific details and applications may involve additional considerations, such as the interaction with complex biological tissues or materials.

Recent Advancements in SHG Microscopy

Recent advancements in SHG microscopy have expanded its capabilities and improved its performance. One notable development is the integration of multiphoton microscopy techniques, such as two-photon excited fluorescence (TPEF) and third harmonic generation (THG), into a single imaging platform. This multimodal approach allows researchers to simultaneously acquire complementary information from different contrast mechanisms, enhancing the overall imaging depth and specificity.

Furthermore, advances in laser technology and detection systems have contributed to the improvement of SHG microscopy. Ultrafast lasers with higher repetition rates and shorter pulse durations have enabled faster imaging speeds, reducing photodamage and making real-time imaging of dynamic processes feasible.

The incorporation of advanced image processing algorithms has also enhanced the quantitative analysis of SHG data. Automated segmentation and three-dimensional reconstruction algorithms facilitate the extraction of valuable information from complex biological structures, providing researchers with more detailed and accurate insights.

Challenges and Future Perspectives

Despite its remarkable capabilities, SHG microscopy faces certain challenges. One limitation is the need for a strong SHG signal, which restricts its applicability to tissues rich in nonlinear structures. Strategies to enhance the SHG signal, such as optimizing laser parameters and using contrast agents, are areas of ongoing research.

Another challenge is the limited penetration depth of SHG microscopy in highly scattering tissues. While SHG signals can be generated deep within tissues, scattering of emitted photons can hinder their detection. Advanced imaging techniques, such as adaptive optics and novel detection schemes, are being explored to overcome this limitation.

Looking forward, the future of SHG microscopy holds exciting possibilities. Continued advancements in technology, combined with a deeper understanding of nonlinear optical processes in biological tissues, will likely expand the scope of SHG microscopy. Integration with other imaging modalities and the development of miniaturized, portable SHG systems may pave the way for its application in clinical settings.

Final Words

Second Harmonic Generation microscopy has emerged as a valuable tool in the realm of biological imaging, offering high-resolution, label-free visualization of structures within living organisms. Its applications span a wide range of fields, from connective tissue research to neuroscience and cancer biology. Recent advancements have addressed some of the limitations, opening new avenues for exploration.

As technology continues to evolve, the potential for SHG microscopy to contribute to our understanding of complex biological processes remains substantial. By unraveling the mysteries hidden within tissues at the microscopic level, SHG microscopy stands as a testament to the power of interdisciplinary research and technological innovation in advancing our knowledge of the biological world. Please provide your comments below, it will help us in improving this article. Thanks for reading!

Key Figures in Second Harmonic Generation Microscopy

One of the early pioneers in the field of nonlinear optics, including Second Harmonic Generation, is Maria Goeppert-Mayer, who was awarded the Nobel Prize in Physics in 1963 for her work on nuclear structure. However, her contributions are more related to the broader field of nonlinear optics rather than specifically to SHG microscopy.

The development of SHG microscopy as a technique for biological imaging gained momentum in the late 20th century and early 21st century. Scientists like Watt W. Webb, Winfried Denk, and Paul W. Wiseman have played significant roles in advancing SHG microscopy and its applications in the biological and biomedical sciences. Webb, in particular, is often associated with the development of multiphoton microscopy techniques, including SHG microscopy.

Key Discoveries using Second Harmonic Generation Microscopy

  1. Collagen Fiber Organization: SHG microscopy has been instrumental in unraveling the intricate structure and organization of collagen fibers in biological tissues. It has provided unprecedented details about collagen architecture in tissues like skin, tendons, and cornea.

  2. Muscle Contraction and Sarcomere Dynamics: Studies using SHG microscopy have revealed detailed information about muscle contraction and the dynamics of sarcomeres, the basic functional units of muscle tissue. Researchers have gained insights into the structural changes occurring during contraction and relaxation.

  3. Neuronal Imaging: SHG microscopy has been applied to study neuronal structures and their interactions. Researchers have used SHG to visualize myelinated nerve fibers and study the morphology of axons in the nervous system.

  4. Bone Tissue Imaging: SHG microscopy has been employed to investigate bone tissue at the microscopic level. It has provided information about the mineralization process, collagen organization, and the structural changes in bone associated with diseases like osteoporosis.

  5. Cell Division and Cytoskeletal Dynamics: SHG microscopy has allowed researchers to observe and analyze cell division processes, providing insights into the dynamics of the cytoskeleton. This includes the visualization of microtubules and other cytoskeletal components during mitosis.

  6. Cancer Research: In cancer research, SHG microscopy has played a crucial role in studying the collagen alterations associated with tumor progression. It has enabled the characterization of the tumor microenvironment and the identification of potential biomarkers.

  7. Biomedical Applications: SHG microscopy has found applications in label-free imaging of biological samples. This is particularly valuable in studying live cells and tissues without the need for exogenous contrast agents.

  8. Dermatology and Wound Healing: SHG microscopy has been used to study skin structure and wound healing processes. It has provided insights into the remodeling of collagen in scar tissue and the dynamics of collagen fibers during the healing process.

  9. Nanomaterial Characterization: SHG microscopy has been applied in materials science to characterize nanomaterials and nanostructures. Researchers have used SHG to study the surface properties, crystallinity, and organization of nanomaterials.

  10. Advancements in Multiphoton Imaging: SHG microscopy has contributed to the broader field of multiphoton imaging. It has been integrated with other modalities, such as two-photon excited fluorescence, enabling researchers to obtain complementary information from biological samples.

Second Harmonic Generation Microscopy

Hardware and software required for Second Harmonic Generation Microscopy


  1. Laser Source:

    • Ti:sapphire Laser: Commonly used for SHG microscopy due to its tunability and short pulse duration.
    • Other Femtosecond Lasers: Depending on the application and requirements, other lasers like fiber lasers may be used.
  2. Microscope System:

    • Objective Lens: High numerical aperture (NA) objectives for high-resolution imaging.
    • Scanning System: To raster-scan the laser beam over the sample.
    • Detection System: Photomultiplier tubes (PMTs), avalanche photodiodes (APDs), or other detectors sensitive to the SHG signal.
  3. Nonlinear Crystal:

    • Beta Barium Borate (BBO) Crystal: Commonly used for SHG due to its high nonlinear coefficient.

  4. Optical Filters:

    • Bandpass Filters: To isolate the SHG signal and block unwanted wavelengths.
    • Emission Filters: Specific filters to allow only the SHG wavelength to reach the detectors.
  5. Polarization Optics:

    • Polarizers and Waveplates: Used to control and optimize the polarization of the laser beam.

  6. Beam Splitter:

    • Dichroic Beam Splitter: To separate the SHG signal from the excitation light.

  7. Detector:

    • Photodetectors: Photomultiplier tubes (PMTs) or avalanche photodiodes (APDs) are commonly used for detecting the SHG signal.

  8. Stage:

    • Motorized Stage: Allows precise movement and positioning of the sample.

  9. Control and Data Acquisition System:

    • Computer: To control the microscope, acquire images, and run data analysis.
    • Data Acquisition Card: To interface with detectors and control the scanning system.


  1. Microscopy Control Software:

    • Microscope Software: Commercial or custom software to control the microscope components, including laser power, scanning, and image acquisition.

  2. Image Analysis Software:

    • Fiji/ImageJ: Widely used open-source software for image processing and analysis.
    • MATLAB or Python with Scientific Libraries: Custom scripts or programs for advanced data analysis.
    • CellProfiler: Specialized software for cell image analysis.
  3. 3D Reconstruction Software:

    • Imaris: Enables three-dimensional reconstruction and visualization of SHG images.
    • Bitplane Fiji: Fiji distribution with additional plugins for 3D reconstruction.
  4. Data Visualization and Presentation:

    • Graphing Software: Such as Origin or Gnuplot for visualizing and presenting data.
    • Adobe Creative Suite or Inkscape: For creating figures and illustrations.
  5. Machine Learning Tools:

    • Python Libraries (e.g., scikit-learn): If machine learning is applied for image analysis.

  6. Additional Analysis Tools:

    • Statistical Software: R or SPSS for statistical analysis if needed.

  7. Documentation and Reporting:

    • Microsoft Office or LaTeX: For preparing reports and scientific publications.

Facts on Second Harmonic Generation Microscopy

Nonlinear Optical Process: SHG is a nonlinear optical process that occurs when two photons of the same frequency interact with a nonlinear material, resulting in the generation of a new photon with double the frequency and half the wavelength (second harmonic).

Label-Free Imaging: SHG microscopy is a label-free imaging technique, meaning it does not require exogenous contrast agents or fluorescent labels. It relies on the intrinsic properties of the sample, particularly those with non-centrosymmetric structures like collagen fibers.

Collagen Imaging: One of the primary applications of SHG microscopy is the imaging of collagen fibers in biological tissues. Collagen, a major structural protein in connective tissues, exhibits a non-centrosymmetric arrangement, making it a strong source of SHG signals.

High Spatial Resolution: SHG microscopy provides high spatial resolution, allowing researchers to visualize structures at the submicron level. This capability is crucial for studying fine details in biological tissues, such as cell membranes, fibrillar structures, and organelles.

Three-Dimensional Imaging: SHG microscopy enables three-dimensional imaging of biological samples. By acquiring serial optical sections at different depths, researchers can reconstruct a 3D representation of the sample, providing a comprehensive view of its structure.

Biomedical and Clinical Applications: SHG microscopy has found applications in various biomedical and clinical studies. It has been used to investigate diseases like cancer, study wound healing processes, and understand the structural changes in tissues associated with different pathologies.

Multiphoton Imaging Integration: SHG microscopy is often integrated with other multiphoton imaging modalities, such as two-photon excited fluorescence (2PEF). This multimodal approach allows researchers to gather complementary information from samples, enhancing the overall imaging capabilities.

Material Science Applications: In materials science, SHG microscopy is employed to study the crystalline structure and organization of materials at the microscopic level. It has applications in characterizing nanomaterials, thin films, and other materials with nonlinear optical properties.

Advancements in Technology: Ongoing technological advancements have led to the development of advanced SHG microscopy techniques, including polarization-resolved SHG, spectral SHG, and various nonlinear imaging modalities. These advancements contribute to improved imaging capabilities and data extraction.

In Vivo Imaging: SHG microscopy has been successfully applied to in vivo imaging, allowing researchers to study biological processes and structures in living organisms. This capability is valuable for longitudinal studies and real-time observations in a physiological context.

Quantitative Analysis: SHG microscopy enables quantitative analysis of the generated signals. This includes measuring signal intensities, polarization properties, and other parameters, providing researchers with quantitative insights into the sample’s characteristics.

Photodamage Minimization: Compared to traditional imaging techniques, SHG microscopy often involves lower levels of photodamage to samples. The use of near-infrared light and the nonlinear nature of the process contribute to reduced photobleaching and phototoxicity.

Academic References on Second Harmonic Generation Microscopy

  1. Campagnola, P. J., & Dong, C. Y. (2005). Second harmonic generation microscopy: principles and applications to disease diagnosis. Laser & Photonics Review, 5(1), 13-26.

  2. Zipfel, W. R., Williams, R. M., & Webb, W. W. (2003). Nonlinear magic: multiphoton microscopy in the biosciences. Nature Biotechnology, 21(11), 1369-1377.

  3. Plotnikov, S. V., Millard, A. C., Campagnola, P. J., & Mohler, W. A. (2006). Characterization of the myosin-based source for second-harmonic generation from muscle sarcomeres. Biophysical Journal, 90(2), 693-703.

  4. Chen, X., Nadiarynkh, O., Plotnikov, S., & Campagnola, P. J. (2012). Second harmonic generation microscopy for quantitative analysis of collagen fibrillar structure. Nature Protocols, 7(4), 654-669.

  5. Débarre, D., Supatto, W., & Beaurepaire, E. (2006). Structure sensitivity in third-harmonic generation microscopy. Optics Letters, 31(2), 275-277.

  6. Cheng, J. X., & Xie, X. S. (2002). Coherent anti-Stokes Raman scattering microscopy: instrumentation, theory, and applications. Journal of Physical Chemistry B, 106(35), 8493-8503.

  7. Kim, P., Puoris’haag, M., Côté, D., Lin, C. P., & Yun, S. H. (2008). In vivo confocal and multiphoton microendoscopy. Journal of Biomedical Optics, 13(1), 010501.

  8. Roth, S., Freund, I., & Deutsch, M. (1986). Second harmonic generation in collagen. Journal of Chemical Physics, 84(2), 1312-1317.

  9. Stoller, P., Reiser, K. M., Celliers, P. M., & Rubenchik, A. M. (2002). Polarization-modulated second harmonic generation in collagen. Biophysical Journal, 82(6), 3330-3342.

  10. Débarre, D., Olivier, N., & Beaurepaire, E. (2005). Signal epidetection in third-harmonic generation microscopy of turbid media. Optics Express, 13(19), 9235-9249.

  11. Chen, S. Y., Wu, H. Y., Sun, Y., Lin, B. S., Lin, Y. F., & Dong, C. Y. (2009). Imaging cells and extracellular matrix in vivo by using second-harmonic generation and two-photon excited fluorescence. Proceedings of the National Academy of Sciences, 109(1), 65-70.

  12. Bu, W., Shi, L., Chen, Y., & Huang, J. (2013). Two-photon-excited fluorescence and second-harmonic generation of semiconductor quantum dots. Journal of the American Chemical Society, 135(11), 4082-4085.

  13. Wokosin, D. L., Centonze, V. E., White, J. G., & Armstrong, W. M. (1996). Polarized three-photon excitation fluorescence microscopy. Journal of Microscopy, 181(2), 160-165.

  14. Brown, C. M., Rivera, D. R., & Pavone, F. S. (2008). Multiphoton fluorescence lifetime imaging of intrinsic fluorescence in human and rat brain tissue reveals spatially distinct NADH binding. Optics Express, 17(2), 984-994.

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