Spheroids and 3D Organoids Cell Cultures: The Main Differences

Spheroids and 3D Organoids Cell Cultures: The Main Differences

In the field of biomedical research, 3D cell cultures have become invaluable, allowing scientists to explore cellular behaviours and interactions in greater depth. The advent of technologies such as spheroid microplates and organ-on-a-chip has facilitated the shift from 2D to 3D cell culture, revolutionizing the way researchers study biological systems. Among these advanced models, spheroids and 3D organoids have stood out for their ability to closely mimic the structure and function of tissues and organs, which traditional 2D cultures can’t achieve. This blog post explores the distinctive features of spheroids and organoids, pointing out their similarities, differences, and specific uses in research.



In the dynamic landscape of biomedical research, the advent of three-dimensional (3D) cell cultures has revolutionized our ability to study complex biological systems outside the human body. Unlike traditional two-dimensional (2D) cultures, which oversimplify cellular interactions, 3D cultures like spheroids and organoids more accurately mimic the intricate structure and function of tissues and organs. This advancement is crucial for gaining deeper insights into fundamental biological processes, disease mechanisms, and drug responses in a more physiologically relevant context. In the past decade, scientists have developed innovative solutions to cultivate cells in 3D

Spheroids and organoids are at the forefront of this paradigm shift towards 3D cultures. Spheroids, originating from self-assembled cell aggregates, are prized for their simplicity and ability to be scaled up, making them ideal for high-throughput applications such as drug screening and toxicity testing. Conversely, organoids, derived from tissue-specific precursor cells or stem cells, replicate the complex cellular architecture and functionality of organs, making them invaluable for studying organ development, disease modeling, and personalized medicine. Their growing use across various fields highlights their potential to bridge the gap between in vitro studies and medical applications, offering new insights and innovations in biomedical research.

What are Spheroids?

Spheroids are simple, three-dimensional cell clusters that can be made up of either a single cell type or a mixture of different cell types. They have a straightforward architecture. This simplicity, however, doesn’t diminish their value. By providing a 3D environment, spheroids allow cells to interact with each other and their surroundings in ways that are much closer to what happens inside the body compared to traditional 2D cell cultures, where cells grow in a flat single layer, providing a more physiologically relevant model.

An illustration of a 3D spheroid with a white background
An illustration of a 3D spheroid.

Spheroids can be produced using various methods, such as the hanging-drop method, ultra-low attachment plates, and microfluidic systems. Their creation and maintenance are relatively easy and scalable, making them ideal for various research applications such as high-throughput drug screening and toxicity testing.

For instance, tumor spheroids are widely used in cancer research to study how tumors grow, spread, and respond to treatments. Stem cell spheroids are valuable in regenerative medicine, helping scientists understand how stem cells differentiate and can be used in tissue engineering. Additionally, hepatocyte spheroids are important in liver research, particularly for testing drug toxicity and metabolism.

What are Organoids?

Organoids are tiny, three-dimensional structures grown from stem cells that replicate much of the complexity of real organs. These miniature versions can develop from pluripotent or adult stem cells, organizing themselves into tissue architectures similar to those of their parent organs. They contain multiple cell types that interact in a way that mimics natural tissues, making them invaluable for research.

An illustration of a Pancreatic 3D Organoid with a white background.
An illustration of a Pancreatic Organoid.

One of the remarkable aspects of organoids is their ability to self-organize. Through processes like cell sorting and spatially restricted lineage commitment, they can form complex structures in a lab setting. This self-organization leads to a tissue architecture that closely resembles what we see in living organs. Organoids not only look like real organs but also perform many of their functions, such as secretion, absorption, and various metabolic activities.

Organoids can be created from a variety of tissues, including the brain, pancreas, kidney, and intestine. For instance, brain organoids are used to study neurodevelopmental and neurodegenerative diseases, while intestinal organoids are valuable for research on gastrointestinal diseases and drug absorption. Pancreatic organoids are crucial for researching diseases such as diabetes and pancreatic cancer and for drug testing and development. By mimicking the structure and function of real organs, organoids provide a powerful tool for understanding organ development, disease progression, and how different therapies might work.

What is the Difference Between Spheroids and Organoids ?

Spheroids and organoids are often referred to interchangeably. However, they have distinct meanings as they differ significantly in several key aspects, making each suitable for distinct types of research.

Below are presented the main differences between spheroids and 3D organoids cell cultures.

Cellular composition

In terms of cellular composition, organoids are made up of multiple cell types that come together to mimic the complex structure and organization of real tissues or organs. This allows them to closely replicate the cellular architecture of their parent organ. On the other hand, spheroids are primarily composed of a single cell type or a simple mixture of different types, lacking the detailed tissue-specific organization seen in organoids.


When it comes to complexity, spheroids have a simpler structure, unlike organoids, that exhibit a higher level of complexity both in their structural morphology and their functional capabilities.

While spheroids provide a more realistic environment than traditional two-dimensional cultures, they do not possess the advanced morphological and functional features of organoids that can develop intricate, tissue-specific features and perform functions characteristic of the tissues they represent.

Size and scalability

Regarding size and scalability, organoids are generally larger, sometimes even reaching macroscopic sizes. Spheroids, being simpler and smaller, are easier to manage and culture in large quantities. Their straightforward culture requirements make them ideal for high-throughput applications where scalability is essential.

Cultural conditions and timeline

Spheroids can be cultured with or without extracellular matrix (ECM), as some cells generate their own ECM during formation and require only growth factors. This flexibility allows spheroids to form relatively quickly, typically within 2-3 days.

In contrast, organoids have a longer culture timeline as they require specific growth conditions and nutrients. They often need the addition of ECM and supplementary growth factors to support their complex development and maintain their structures. This results in a longer culture timeline for organoids, often taking 21-28 days or more to develop fully, reflecting their increased complexity.


Maintaining spheroids long-term can be challenging due to their relatively simple structure and lack of self-sustaining systems. Organoids, with their more complex organization and functionality, often exhibit long-term viability, making them suitable for extended studies on organ development and disease progression.

Different Applications of Spheroids and Organoids 3D Cell Cultures

Spheroids and organoids 3D cell cultures play pivotal roles in contemporary biomedical research. They serve as adaptable instruments across multiple scientific disciplines, enabling profound exploration into complex biological phenomena and the refinement of targeted therapeutic approaches. Spheroids and organoids have a wide range of applications as they collectively enhance our comprehension of cellular dynamics, disease pathogenesis, and therapeutic interventions, favoring innovative strides in modern medicine and biological sciences alike.

Applications of Spheroids

Spheroids, with their ease of culture and scalability, have found extensive applications in biomedical research:

  • One of their most notable uses is in cancer research, where tumor spheroids help scientists understand the in vivo microenvironments of tumors, aiding in the prediction of drug efficacy.
  • Additionally, spheroids are widely used in high-throughput drug screening and toxicity testing, providing a more realistic 3D context that better represents the in vivo environment compared to traditional 2D cultures.
  • They also play a crucial role in studying cell-cell interactions and the effects of environmental factors such as chemicals and radiation on cell behavior and viability.
  • Furthermore, in stem cell research, spheroids are used to develop embryoid bodies from induced pluripotent stem cells, which can be differentiated into high-purity neural stem cells for studying neural diseases and potential treatments.

Applications of Organoids

Organoids, on the other hand, are particularly suitable for more complex and specialized applications due to their high complexity and functionality:

  • In disease modeling, organoids are used to replicate various diseases, including cancer and genetic disorders, offering deep insights into disease mechanisms and potential treatments.
  • They are invaluable in drug discovery and personalized medicine, enabling the testing of drug efficacy and toxicity on patient-specific cells, which paves the way for specific treatment plans.
  • Organoids also significantly contribute to understanding developmental biology, helping researchers study organ development processes and the effects of genetic mutations. In cancer research for example, 3D organoids provide insights into the mutational signatures of selected cancers by mimicking the pathophysiology of human tumors.
  • Moreover, organoids play a vital role in CRISPR research (Clustered Regularly Interspaced Short Palindromic Repeats), a powerful tool for editing genomes, aiding scientists in studying organ development within the context of gene editing. For instance, neural organoids are advancing our understanding of brain diseases, bringing researchers closer to deciphering the complexities of neurological conditions.


Visual RepresentationAn illustration of a 3D spheroid with a white backgroundAn illustration of a Pancreatic Organoid with a white background.
DefinitionSimple, rounded-spheres, three-dimensional cell clustersTiny, three-dimensional structures grown from stem cells
Cell Type CompositionPrimarily composed of a single cell type or a mixtureComposed of multiple cell types mimicking real organs
Structural ComplexitySimpler structureHigh complexity with detailed tissue-specific features
DiversityLimited diversityMimic the diversity of organs
Tissue-Specific OrganizationLacks intricate tissue-specific organizationClosely replicates the cellular architecture of parent organs
FunctionalityLimited functionalityPerforms functions characteristic of the tissues they represent
SizeGenerally smallerGenerally larger, sometimes macroscopic
ScalabilityEasier to manage and culture in large quantitiesMore complex to culture and maintain
Culture ConditionsCan be cultured with or without ECM; requires only growth factorsOften requires ECM and supplementary growth factors
Culture TimelineForms relatively quickly (2-3 days)Longer culture timeline (21-28 days or more)
MaintenanceChallenging to maintain long-termOften exhibits long-term viability
ApplicationsHigh-throughput drug screening, toxicity testing, studying cell-cell interactions, and environmental effectsDisease modeling, drug discovery, personalized medicine, understanding developmental biology, and CRISPR research
ExamplesTumor spheroids, stem cell spheroids, hepatocyte spheroidsBrain organoids, intestinal organoids, pancreatic organoids
Cancer ResearchHelps understand tumor microenvironments and predict drug efficacyProvides insights into mutational signatures and pathophysiology of tumors
Stem Cell ResearchDevelops embryoid bodies from induced pluripotent stem cellsAids in studying organ development and gene editing


Spheroids and organoids represent critical advancements in 3D cell culture technologies, and are valuable tools in biomedical research. Together, they have significantly advanced our understanding of human biology and disease mechanisms and have facilitated breakthroughs in drug discovery. Looking ahead, the future of 3D cell culture technologies promises even more sophisticated models. These advancements will likely enhance the accuracy and relevance of experimental models, enabling researchers to study complex biological processes and accelerating the development of novel therapies. 

Stay tuned for more in-depth insights, informative articles, and practical applications in our upcoming posts. Until then, keep exploring the fascinating world of biomedical research and discovery! 🧬✨

📧 If you have any questions or feedback, please feel free to contact us at contact@darwin-microfluidics.com.


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