Microscopy in Mycology

Microscopy in Mycology

Learning Microscopy for Mycology

Discover the world of microscopy with me, a doorway that's unveiling the intricate secrets of mycology. Here, every minute detail from the phases of mushroom growth to the nuances of spore formations is magnified and brought to the forefront. As I navigate this journey, teaching myself the art of microscopy, I'm fueled by an insatiable curiosity to enhance my mycology understanding. Imagine unraveling the stages of the mushroom lifecycle or observing the intricate web of mycelial structures, all waiting to be discovered under the lens. But to truly appreciate this micro-realm, we first need to familiarize ourselves with the tools of observation: microscopes. Let's embark on this voyage of microscopic wonder together.

Different Types of Microscopes

Microscopes have evolved over time, each type designed to serve specific purposes and offer unique insights into the microscopic world. Here are some commonly used microscopes:

  • Compound Light Microscope: This microscope uses visible light and a system of lenses to magnify images of small samples. They are ideal for observing cells, spores, and other microscopic details of fungi. The specimen is typically viewed on a flat slide and illuminated from below, allowing for the observation of thin slices or sections.
  • Stereo Microscope: Also known as a dissecting microscope, it provides a three-dimensional view of larger specimens, like mushroom caps or parts of fungi. This type uses two separate optical paths for each eye, offering a broader field of view and depth perception, making it perfect for surface details.
  • Electron Microscope: Unlike optical microscopes, electron microscopes use a beam of electrons to create an image of the specimen. They offer extremely high resolution and magnification, allowing researchers to view structures at a molecular level. Two primary types are the Transmission Electron Microscope (TEM) and the Scanning Electron Microscope (SEM).
  • Phase Contrast Microscope: This microscope enhances the contrast of transparent and colorless specimens by utilizing the phase differences of light waves. It's especially useful for viewing intracellular structures in fungi, like nuclei and vacuoles, which may not be visible with standard light microscopy.
  • Fluorescence Microscope: Utilizing fluorescent stains and specific wavelengths of light, this microscope allows researchers to visualize specific structures or molecules within fungal cells. The fluorescent molecules absorb light at one wavelength and then re-emit it at another, making them glow against a dark background.
  • Confocal Microscope: An advanced optical imaging technique, the confocal microscope uses point illumination and a pinhole to eliminate out-of-focus light in specimens that are thicker than a typical light microscope slide. This results in clearer images with better depth resolution, making it especially useful for three-dimensional reconstructions of fungal structures.
  • Differential Interference Contrast (DIC) Microscope: This microscope enhances contrast by superimposing a split beam of light that has passed through the sample. The two beams interfere with each other, resulting in an image with a shadowy, three-dimensional appearance. It’s especially valuable for observing the fine structures of fungal cells without staining.

For hobbyists and those venturing into mycology, the Compound Light and Stereo Microscopes offer affordability without compromising on quality.

Which Microscope to Buy?

If you're a beginner stepping into the world of microscopy, expect to invest anywhere between $100 to $500 for a reliable starter microscope. When shopping, prioritize clarity, build quality, and user-friendly features. It's essential to avoid microscopes that feel too lightweight or those with plastic lenses, as these can hinder the viewing experience. I personally use the Swift SW380T Compound Microscope, which, though leaning towards the higher end of introductory scopes, offers impeccable clarity and durability, making it a worthwhile investment for any budding mycologist.

Microscope Buying Guide

When considering a microscope for mycology, keep these features in mind:

  • Magnification: Most hobbyist microscopes offer a range from 40x to 1000x.
  • Objective Lenses: Ensure they are of good quality. Achromatic lenses reduce color distortion.
  • Illumination: LED lighting is ideal due to its longevity and consistency. A light with adjustable intensity can be beneficial.
  • Mechanical Stage: This allows for precise movement of the slide, which is especially handy at higher magnifications.
  • Focusing: Fine and coarse focusing knobs can make the experience smoother.
  • Build Quality: A solid build ensures durability and stability while working.
  • Anatomy of a Trinocular Compound Microscope

    The image you're viewing is a detailed layout of the Swift SW380T Compound Microscope, a state-of-the-art instrument designed to bring the microscopic world into clear, enlarged view. Each labeled part has a specific function that contributes to the overall performance and precision of the microscope. As you explore the various components, you'll gain a deeper understanding of how this intricate device functions. This particular microscope is the one I am personally learning on, offering both professional-grade features and user-friendly operation.

    Trinocular Compound Microscope Anatomy
    This is my Swift SW380T Compound Microscope.


    Mircoscope Eyepeices

    The eyepiece, often referred to as the ocular lens, is the point where you rest your eye to view the magnified specimen. Typically, the eyepiece will amplify the image by a factor of 10x, although different magnifications are available. It's important to ensure that the eyepiece is clean and free from smudges for the best viewing experience.

    Camera Port

    The camera port is a specialized attachment point that allows you to connect a camera to the microscope. This is especially valuable for researchers and enthusiasts who wish to document their findings, capturing sharp still images or detailed videos of the microscopic world.

    Trinocular Head

    Unique to trinocular microscopes, the trinocular head accommodates the eyepieces and provides a pathway for light. Its tri-observational design has two channels for visual observation and a third dedicated to camera attachments, ensuring high-quality imaging without compromising visual clarity.

    Nose Piece

    Acting as a turret, the nose piece rotates to house multiple objective lenses. This rotation capability allows users to swiftly switch between different lenses, optimizing magnification levels based on the specimen's requirements.

    Objective Lens

    Mircoscope Objective Lenses

    The objective lenses are the heart of magnification. Each lens, secured on the nose piece, offers varying magnification levels. These lenses gather light from the specimen and magnify the image into the eyepiece for observation.

    Slide Holder

    This crucial component ensures stability by gripping the microscope slide. Its design ensures that the slide remains stationary, eliminating any risk of shifts or disturbances during meticulous observations.


    Often crafted from sturdy materials, the arm is the microscope's backbone. It provides stability, connecting the microscope's head to its foundational base, and is also where users typically hold the microscope when transporting it.

    Coarse Focus & Fine Focus

    These two adjustment mechanisms cater to the microscope's focusing needs. While the coarse focus rapidly moves the stage for rough focusing, the fine focus knob tweaks the distance minutely, achieving sharp, refined imagery of the specimen.


    This component plays a pivotal role in managing the light's intensity that reaches the specimen. By altering the diaphragm's aperture, users can modify brightness levels, which can greatly impact the image's clarity and contrast.


    Situated below the stage, the condenser works in tandem with the light source. It gathers and focuses the light onto the specimen, ensuring uniform illumination and optimized contrast.

    Light Source

    Modern microscopes typically employ LED lighting due to its bright, cool, and energy-efficient properties. The light source ensures that the specimen is adequately illuminated, rendering it visible in high detail.

    Brightness Control

    Integrated with the light source, this control allows users to tweak the illumination intensity, enabling optimal visibility of various specimens, whether translucent or opaque.

    Mechanical Stage

    This platform provides support and precise positioning for the microscope slide. With its adjustable features, it can be moved horizontally or vertically, ensuring the specimen remains centered and in focus.

    Stage Control

    Microscope Mechanical Stage

    These user-friendly knobs, often located on the microscope's side, grant the ability to shift the mechanical stage in precise increments, offering unparalleled control over the specimen's positioning.

    • Coarse Focus: Roughly transitions the stage up and down, used to begin focusing in on a specimen.
    • Fine Focus: Precisely manipulates the depth of focus.

    Filter Holder

    Situated below the stage, this holder is designed to accommodate various color or specialty filters. By using different filters, viewers can enhance contrast, emphasize specific structures, or deploy unique viewing techniques to augment the observation experience.

    Understanding Magnification

    Magnification is often perceived as the holy grail in microscopy, but it's essential to tread with caution. The prominently showcased magnification by manufacturers isn't always a true reflection of the microscope's capability. In fact, the total magnification is a product of the eyepiece and the objective lens magnifications combined. Marketers, in a bid to flaunt an expansive magnification spectrum, frequently include rarer 25x eyepieces or 100x oil immersion objectives.

    However, there's a catch. As you climb the magnification ladder, particularly with the eyepiece, the crispness of the image can wane. This explains my reluctance to use the 25x eyepieces accompanying my microscope. I'd illustrate the contrasting image quality, but my camera phone adapter is at odds with the 25x eyepiece, adding to its list of shortcomings.

    On the topic of oil immersion objectives, they require immersion in a designated oil to unlock their high magnification potential. But it's a double-edged sword: the oil, while facilitating a detailed view, is notorious for its messiness and potential harm to non-oil objectives in case of inadvertent contact. Though often unnecessary, the oil immersion does shine in mycology, especially when examining finer structures like hyphae and spores.

    Magnification Chart





    4x 20x 40x 64x 80x 100x
    10x 50x 100x 160x 200x 250x
    20x 100x 200x 320x 400x 500x
    40x 200x 400x 640x 800x 1000x
    60x 300x 600x 960x 1200x 1500x
    Oil Immersion
    500x 1000x 1600x 2000x 2500x
    Depth of Focus

    Depth of Focus: the distance between the two extreme axial points behind a lens at which an image is judged to be in focus.

    Simply put, as the focus knobs are manipulated up and down, the focus (sharpest layer) rolls up and down the specimen.

    Carolyn Grayson created a great video demonstrating depth of focus using three different colors of tread stacked on top of each other.

    Understanding Lighting & Filters in Microscopy

    Compound microscopes primarily use bottom illumination, where light emanates from a source beneath the specimen and then travels through the specimen, eventually reaching the microscope optics. Modern LED light sources offer distinct advantages over traditional ones due to their energy efficiency, minimal heat production, and longevity.

    Many microscopes come equipped with a filter holder, granting users the ability to adjust the specimen's color or even the backdrop's hue. For budget-conscious enthusiasts, 3D printed filter sets are readily available on platforms like eBay.

    Various Microscopy Techniques

    Darkfield Filter
    Darkfield Technique

    Enhances specimen visibility by illuminating it with light from the side, contrasting it against a dark background.

    Rheinberg Filter
    Rheinberg Illumination

    Allows for color variation in both specimen and background, offering a vivid microscopy experience.

    Oblique Filter
    Oblique Lighting

    Illumination from a side angle produces a three-dimensional appearance by heightening image contrast.

    Capturing the Micro World: Photography Through Microscopes

    In today's digital age, documenting and sharing microscopic observations has become increasingly popular, catering to both scientific documentation and social media shares. With trinocular head microscopes featuring camera ports, capturing these minuscule wonders has never been easier. However, for those without such features, smartphone adapters offer a feasible alternative.

    Smartphone Camera Adapters

    If you're on a budget, smartphone adapters are a practical choice. All the microscopic images showcased here were captured using a phone adapter. If you're considering this route, ensure the adapter is compatible with your phone model and fits snugly over your microscope's eyepiece.

    SLR Camera Adapters

    For those who already possess an SLR camera, specialized adapters are available to connect your camera directly to the microscope's camera port or photo tube. As with any accessory, it's essential to verify the adapter's compatibility with your specific camera model before purchasing.

    Dedicated Microscope Cameras

    There are cameras designed exclusively for microscopy. These cameras ensure the highest quality images and videos of your microscopic findings. However, they often come with a hefty price tag, sometimes even exceeding the cost of the microscope itself. For those just starting or on a tighter budget, it might be wise to consider using one of the above-mentioned adapters before making a substantial investment in a dedicated microscope camera.

    Microscopic Observations
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