3D Biology: Imaging, Automation, and Analysis of 3D Cell Models
Three‑dimensional cell models, including spheroids and organoids, are increasingly used to study biological processes in more physiologically relevant contexts. Working with these models introduces distinct considerations for imaging, automation, and data analysis.
Enabling scalable and reproducible workflows in 3D biology
3D biology refers to the study of cells grown in three‑dimensional structures, such as spheroids or organoids, rather than traditional two‑dimensional cultures. Because these models more closely reflect biological organization, they introduce practical considerations for sample handling, imaging, and data analysis. Compared with 2D culture, 3D biology workflows must account for increased biological variability and more complex experimental designs.
These models can introduce additional complexity in sample handling, imaging, and data analysis. As researchers move from 2D to 3D cell culture, workflows often need to support greater biological variability, increased assay complexity, and higher data volumes. Scalable and reproducible 3D biology workflows typically rely on integrated approaches to culture, imaging, and analysis.
The following sections outline key technologies commonly used to support 3D biology experiments
Key technologies that support 3D biology experiments
The CellXpress.ai® Automated Cell Culture System
The CellXpress.ai Automated Cell Culture System is designed to automate selected cell culture processes used in 3D biology workflows, including monitoring, feeding, and expansion, with the goal of supporting consistency over extended culture periods.
The 3D Ready® Organoid Expansion Service
The 3D Ready Organoid Expansion Service supports the generation and expansion of quality-controlled organoids at scale, leveraging proprietary bioreactor and bioprocess technology to produce reliable and predictive PDOs.
https://share.vidyard.com/watch/zbx5hvfDZWnGzvrWpoM9id
Dr. Oksana Sirenko, Sr. Scientist, explains how 3D cell models and high-content imaging are helping to advance Drug Discovery
End‑to‑end support for automated 3D biology workflows
Molecular Devices supports researchers implementing automated 3D biology workflows in laboratory settings, with the goal of enabling scalable and consistent use of 3D cell models through system integration, optimization, and workflow support.
These workflows commonly combine the following components:
Why researchers are moving from 2D to 3D cell models
The revolutionary promise of 3D Biology
We believe organoids are the future of next-gen drug discovery, offering revolutionary promises to reduce drug development timelines, overcome limitations of conventional cell models, and move us away from animal research.
Are you ready to transition from 2D to 3D biology, but not sure where to start? In our latest blog, we show you what it takes to enter into this new drug discovery paradigm.
Automated cell culture to support 3D biology workflows
An AI‑driven cell culture innovation hub designed to automate processes and support workflow execution using machine learning‑assisted monitoring, feeding, imaging, and scheduling.
It’s a revolutionary system that gives your team total control over demanding feeding and passaging schedules—reducing hands-on time in the lab while maintaining a 24/7 schedule for growing and scaling multiple PDO/iPSC cell lines, spheroids, or organoids.
The CellXpress.ai cell culture platform supports automation of routine cell culture tasks and integrates monitoring and reporting functions that can be applied across long‑term 3D culture workflows, including organoid‑based processes.
Organoid Expansion Services for 3D Cell Culture Experiments
Quality-controlled organoids are manufactured at scale, leveraging proprietary bioreactor and bioprocess technology to produce reliable and predictive PDOs.
Molecular Devices has global leadership in the scale-up and industrial manufacture of human-derived 3D organoids. Facilitated by our unique, patent-pending bioprocess technology, our semi-automated procedure uses controlled, monitored conditions to produce large numbers of standardized patient-derived organoids (PDOs) within a defined size range. Rigorous quality control ensures reduced batch-to-batch and user-to-user variability.
We offer the capability to scale up your proprietary organoid lines to meet your specific requirements.
Frequently asked questions about 3D biology
What is 3D biology?
3D biology refers to the study of cells grown in three‑dimensional structures, such as spheroids or organoids, rather than traditional two‑dimensional cultures. These models are used to better represent cellular organization and interactions observed in biological systems.
How does 3D biology differ from traditional 2D cell culture?
In traditional 2D cell culture, cells grow on flat surfaces, while 3D biology involves cells organized in three‑dimensional structures. This difference can influence cell morphology, behavior, and interactions within experimental models.
Why is there increasing interest in using 3D cell models in preclinical research?
3D cell models are increasingly used because they can better reflect key aspects of tissue biology—such as three‑dimensional architecture, cell–cell interactions, and microenvironmental effects—than traditional 2D cultures. As a result, 3D models often generate more physiologically relevant measurements and may strengthen translational relevance when evaluating drug responses in preclinical research.
What types of 3D cell models are commonly used in 3D biology research?
Common 3D cell models include spheroids, organoids, and organ‑on‑a‑chip systems. Organoids span a wide range of tissue types commonly studied in research, including brain, intestinal, lung, retinal, and tumor models. These 3D structures are widely used to investigate cellular organization and biological processes in physiologically relevant three‑dimensional contexts.
What challenges are associated with working in 3D biology?
Common challenges in 3D biology include establishing consistent and reproducible culture models—particularly at scale—as well as imaging and analyzing three‑dimensional structures. The increased complexity of 3D cell models can introduce additional variability in sample preparation, imaging depth, and downstream data analysis.
How are 3D cell models imaged and analyzed?
Imaging and analysis of 3D cell models typically involve automated imaging systems, including confocal modalities, which enable optical sectioning of complex three‑dimensional structures. Software tools are used to reconstruct and quantify imaging data, while plate‑based assays measured on microplate readers are commonly applied to assess functional endpoints such as viability.
How does Molecular Devices support 3D biology research workflows?
Molecular Devices provides technologies and services that support automated cell culture, imaging, and analysis used in 3D biology experiments, helping researchers implement integrated laboratory workflows.
Is this page intended for product selection or general education?
This page is intended to provide an educational overview of 3D biology and to describe how Molecular Devices technologies are used within 3D biology research workflows. It is not a detailed product specification page.
Do 3D biology experiments require specialized systems?
Many 3D biology experiments use specialized tools for cell culture, imaging, and analysis, depending on experimental design and research requirements.
Organoid Innovation Center Supporting 3D Biology Methods
Streamline end‑to‑end workflows using next‑generation automation integrated into 3D biology laboratory environments.
The Organoid Innovation Center gives visitors real world insight into an automated lab environment and demonstrates how complex 2D and 3D protocols integrate into an end-to-end automated workflow.
Molecular Devices adds proprietary patient-derived organoid technology with acquisition of Cellesce
Molecular Devices expands global R&D hub in Austria
Molecular Devices and HeartBeat.bio announce collaboration to automate and scale cardiac organoids for high-throughput screening in drug discovery
Molecular Devices continues investment in Organoid Innovation Center adding cell engineering capabilities to automated 3D cell culture platform
Molecular Devices opens Organoid Innovation Center
Featured Research & Applications
3D Cell Models
Development of more complex, biologically relevant, and predictive cell-based assays for compound..
Organoids
Organoids are three-dimensional (3D) multi-cellular, microtissues derived from stem cells that..
Organ-on-a-chip
Organ-on-a-chip (OoC) is a technology that uses microfabrication techniques to create..
Patient-derived organoids (Tumoroids)
The use of patient-derived tumor tissue has transformed the field of drug and target..
Cancer Research Solutions
Cancer involves changes which enable cells to grow and divide without respect to normal limits, to...
Stem Cell Research
Stem cells provide researchers with new opportunities to study targets and pathways that are more...
Drug Discovery and Development
The drug discovery landscape is shifting, with more scientists centering cell line development..
Cell Line Development
Stable cell lines are widely used in a number of important applications including biologics (e.g....