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How to Get Deeper Insights into your Organoid and Spheroid Models

Unleashing the power of microscopy for 3D cell culture imaging

Murine esophageal organoids (DAPI, Integrin26-AF 488, SOX2-AF568) imaged with the THUNDER Imager 3D Cell Culture. Courtesy of Dr. F.T. Arroso Martins, Tamere University, Finland.   THUNDER_Imager_3D_Cell_Culture_Murine-esophageal-organoid_LVCC.jpg

In this eBook, learn about key considerations for imaging 3D cell culture models such as organoids and spheroids. Discover innovative microscopy solutions that can shed new insights into dynamic processes in organoids and spheroids in real-time. Through in-depth case studies, we show how these solutions are helping to empower scientists to make new advances in areas such as regenerative medicine, drug discovery, and disease research.


Key Learnings:

  • Key considerations for imaging organoids and spheroids
  • Solutions for examining dynamic processes in organoids and spheroids in real-time
  • Going deeper into 3D with correlative light and electron microscopy (CLEM)


In recent years, the life science research field has undergone remarkable advancements with the emergence of three-dimensional (3D) cell culture systems, including organoids and spheroids.

The potential applications of such 3D model systems are extensive. Because of their more physiologically relevant nature, they can allow researchers to better study physiological processes such as development, homeostasis, regeneration, and disease – including the mechanisms underlying drug resistance. In biopharma, they are indispensable tools for disease modelling, used for identification and evaluation of potential drug candidates. The use of these model systems can also reduce the need for animal models. 

As scientists delve deeper into the intricacies of spheroids, they gain insights that help drive advancements in regenerative medicine and our understanding of complex biology The translatable insights that these model systems can offer has particularly benefited research into cancer, neurodegenerative disease, and immunological disorders.

Organoids and spheroids under the microscope

Microscopy plays a crucial role in studying organoids and spheroids, revealing details of cellular structures, interactions within the microenvironment and live cell dynamic processes. Imaging these models however does present unique challenges. 

Their compact and complex nature often defies conventional imaging techniques, impeding efforts to capture the entirety of the spheroid or obtain high-resolution images of its constituent cellular components. The analysis of spatial cell distribution within an organoid or spheroid, and the quantification of cellular interactions, requires specialized imaging and computational tools. 

In this eBook, we explore some of the challenges encountered when imaging these types of 3D models, shedding light on innovative microscopy solutions that can empower scientists to make new advances in areas such as regenerative medicine, drug discovery, and disease research.

We focus on several case studies including:

  • Examining ‘Brains-In-A-Dish’ from induced pluripotent stem cells (iPSCs)
  • Observing 3D cell cultures during development
  • Developing heart pacemaker cells from cardiac spheroids

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