Posted by Fred Koenig on Mar 10th 2022

Cannabis Farming and Microscopy

Microscopes are increasingly being used in a variety of cannabis industry applications. Dispensaries, growing, and new measurement services programs for forensic cannabis laboratories are increasing nationwide. These laboratories, as well as the farming of cannabis, have opened new fields of microscopy.

The following are the most common uses for microscopy within the cannabis industry:

  • Pathogen identification
  • Quality assurance
  • Potency
  • Law enforcement Investigation

Pathogen Identification

Cannabis is a valuable multipurpose crop with nutritional, medicinal, and industrial uses. Its leaves and flowers produce a spectrum of biologically active secondary metabolites; seeds are a source of nutritious oil and protein. The stem contains two types of fiber that serve as feedstock for the manufacturing of many bio-based consumer goods.

Traditionally, indoor cannabis cultivators have depended on cuttings from a mother plant to produce genetically similar plants. However, it has been observed that over time, the plants become less vigorous and that the mother plants are susceptible to pests and diseases, which the resulting cuttings can harbor these diseases in production spaces.

As cannabis is grown much like any other plant, it is susceptible to infections due to plant pathogens. These pathogens reduce the growth of the crop by affecting roots, crowns, and foliage. In addition, fungi that colonize the inflorescences (or buds) during development or harvest colonize internal tissues, and endophytes (an endosymbiont, often a bacteria or fungus) can significantly reduce the product quality.

Alternatively, in vitro techniques with microscopy offer innovative approaches for both mass production and germplasm maintenance. Micropropagation can also facilitate higher throughput propagation in many species and form the basis of disease-free plants for certified clean plant programs.

Quality Assurance

Quality control (QC) and standardized testing are essential within the legal cannabis industry to meet the increasing demand for safe, high-quality medicinal and recreational products. Growers, producers, and retailers now rely on laboratories to perform accurate and efficient analyses to determine potency, chemovar, and aroma and ensure the end-product does not contain harmful contaminants or pathogens.

In QC labs across the country, analysis is conducted using Chromatography in a combination of microscopy. The basics of chromatography is the separation of compounds achieved by dissolving a mixture in a mobile phase and passing it over a stationary phase.

Recent techniques have been developed and continue to be developed, combining chromatic techniques with microscopy as part of quality assurance involving cannabis.

  • Analytical Chromatography. The most widely used analytical chromatography methods are gas chromatography, liquid chromatography, and high-performance liquid chromatography.
  • Mass spectrometry. MS measures the masses of molecules and chemical compounds within a sample. MS instruments provide greater accuracy for trace-level analysis of mycotoxins and reliable and more robust analysis of pesticide residues and terpenes.
  • Quantitative polymerase chain reaction will identify genes needed to produce CBDA or THCA while identifying microbes, bacteria, or fungus living inside the plant.


Research conducted throughout 2019 and 2020 performed via advanced microscopy has revealed internal structures of cannabis biochemical factories. Cannabis flowers with the most microscopic mushroom-shaped hairs that cover the plant have more cannabinoids and stronger fragrances, determining the potency of the plant.

A study published in The Plant Journal, conducted by researchers from the University of British Colombia (UBC) (1) using a combination of advanced microscope techniques and chemical profiling, examined the internal structures and development of individual microscopic hair, called trichomes. The research findings proved a long-held belief among cannabis enthusiasts that the trichomes hold the richest sources of THC and CBD, forming metabolites and fragrance-giving terpenes.

They found that the stalked trichomes emitted a bright blue color under ultraviolet light and contained a large, distinctive pie-shaped disc of cells. The smaller the sessile trichomes, which did not have a stalk, emitted a red color, had smaller secretory discs and produced fewer fragrant terpenes.

Researchers note that stalked glandular trichomes had expanded cellular factories, growing from sessile-like precursors to undergo dramatic shifts during development that can be visualized using new microscopy tools. As a result, UV light and microscopy could monitor trichome maturity and inform farmers and growers of the optimal harvesting times.

Previous research had identified the three types of glandular trichomes based on their appearance, bulbous, sessile, and stalked—but their relative contributions to the chemical production of cannabis flowers were then unknown.

The researchers also conducted a gene expression analysis to investigate how instructions in trichome DNA are converted into the plant's biochemical products. They found that stalked trichomes were strongly geared toward making cannabidiolic acid (CBDA).

Law Enforcement Investigation

The 2018 Farm bill defined hemp as cannabis containing less than 0.3% TCH and removed hemp from the controlled substances list. As many as 18 states have declared marijuana legal, while another 33 states have made medical marijuana legal. These legal changes have created forensic laboratories across the United States. These laboratories implement quantitive analytical methods to help treat cannabis crops, help determine between seizures are marijuana or hemp, and study the internal structures of cannabis biochemical factories that indicate the potency of cannabis.

There are four groups of cannabis generally categorized:

  • Non-intoxicant
  • Semi-intoxicant
  • Intoxicant
  • Wild

However, the taxonomic classification among these proposed species remains a debated issue. Further complicating matters is the legal distinction between help and drug (narcotic) type cannabis.

Cannabis is one of the most common drugs submitted to crime laboratories across the United States. Due to how similar hemp and cannabis are to one another to the naked eye, crime labs across the country are learning how to distinguish between marijuana from hemp. In order to differentiate between the two after a seizure, crime labs now employ the same procedures as those used in labs to document potency.

Cannabis farming has opened more avenues and new fields for microscopy. As the demand for cannabis products grows, the need for new, innovative microscopy techniques to help ensure quality, potency, and safety for consumers worldwide grows alongside this exciting field of study.