19. April 2023

Biomedical Image Analysis Applications: Spheroids, Organoids & Embryoid Body Analysis

Spheroids, organoids and embryoid bodies are highly valuable 3D culture techniques that are widely used in research for all different kinds of applications. Combined with biomedical imaging and image analysis, those 3D cultures can give valuable insights for research and clinics. Data extracted from biomedical image analysis applications inform researchers of essential biological mechanisms and processes that underpin many diseases and press medical challenges. Thus, innovative medical image processing is necessary to conduct and complete these experiments. Various biomedical image analysis applications rely on high-throughput imaging systems as well as image analysis software ­– especially for complex diseases like cancer, where studying 3D cell culture yields more physiologically relevant information than focusing on single tumor cells.

This blog post will briefly review the differences of 3D cell cultures, including spheroids, organoids, and embryoids and will further discuss why those are used in research. It will also go over various life science solutions to help perform diverse biomedical image analysis applications efficiently and robustly.


Spheroids are simple in-vitro structures produced from one cell type and can mimic specific tissue structures. Because of this benefit, spheroids are good models for cell-to-cell interaction and cancer cell and tumor research [1]. Spheroid formation occurs through self-assembling cell aggregation [1]. 3D spheroid cultures can be maintained longer than single cells and are helpful, for example, for testing the long-term effects of cancer drugs on tumors or understanding neurodegenerative diseases, making spheroids an interesting target of biomedical image analysis [1].


Organoids are complex 3D in vitro clusters consisting of multiple cell types and thereby mimic organs. Those structures are used not only to study organ function [3], but also to give insight into biological systems, including information on an organ’s function, growth, organization, and dynamics. Organoid models are particularly suited for disease research, understanding growth and development in organisms, cell function studies, and drug screening experiments [4]. Biomedical image analysis of those structures can provide direct observation and extraction of quantitative data crucial to the life sciences [4].

Embryoid bodies

Embryonic stem cells aggregate and form embryoid bodies, which can serve as a 3D cell model [5]. Embryoids are valuable in biomedical research because they have the potential to differentiate into a diverse array of specialized cells, and this high level of spontaneous differentiation makes embryoids a prime model of development [5].

TissueGnostics is a leader in developing solutions for biomedical image analysis applications

TissueGnostics has many life science experts that work to develop advanced solutions for biomedical image analysis applications. Specifically, the image analysis software StrataQuest uses machine learning to create complex image algorithms that automatically detect multicellular structures within scanned sections of spheroids, organoids, and embryoids and perform highly detailed contextual tissue analysis [6]. Further, TissueGnostics also provides pre-defined analysis pipelines, called StrataQuest Apps, including the IF Spheroid App which is capable of single cell detection, marker detection as well as spatial analysis.

From capturing processes within the tumor microenvironment to performing image segmentation, the products and services at TissueGnostics will facilitate disease research laboratories in their research workflow and data analysis needs. More information about biomedical image analysis applications can be found online at the TissueGnostics website. If you are interested in learning more about the different biomedical image analysis applications and how they can help to answer your laboratory’s innovative research questions, please reach out to a team member of TissueGnostics today, and they would be happy to assist you. 


TissueGnostics GmbH
Taborstraße 10/2/8
1020 Vienna, Austria
+43 1 216 11 90
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