Microscopy is the foundation of basic biology research. The ability to see biology supports the needs of the scientific community with the visualization, measurement and analysis of cells and particles. It is one of the most ubiquitous piece of equipment found in the life science lab. Specifications can range from simple upright widefield microscopes to powerful confocal fluorescence or super-resolution microscopes.

Fluorescence is the most commonly used way of tagging and identifying single molecule species. The technique uses the luminescence phenomena found in nature to stain entire cells or biomolecules with fluorophores, allowing for the fluorescence microscope to detect the signal, generating both spatial and intensity data. This data is representative of the localization and the amount of the molecules inside a cell. Colocalization and interaction studies can be performed.

Organoids and 3D cell cultures are an exciting development that combines bioengineering with life sciences. Recent advancements have created stable cell cultures in three dimensions, such as organoids, spheroids, or organ-on-a-chip models. 3D cell cultures are grown or printed to mimic the in vivo environment of cells inside the body. Animal cells are embedded in the extracellular matrix (ECM), which is composed of proteoglycans and fibrous proteins. This complex, dynamic, and tissue-specific 3D structure provides physical scaffolding for the cells and initiates cues that influence cell differentiation and behavior.

The majority of cells in living tissue grow, communicate, move, and receive nutrients and oxygen in a physically 3D environment. Therefore, cells behave differently inside a 3D gel matrix compared to a 2D environment. In many cases, a 3D environment reflects the in vivo situation more accurately. This should be considered when analyzing cell behavior, differentiation, response to drug treatment, and gene and protein expression.