Brain Organoids
Organoid technology for understanding brain development and neuronal diseases
Brain organoids: 3D neural models transforming research and discovery
Brain organoids are 3D tissue models derived from human-induced pluripotent stem cells (hiPSCs). When cultured under defined conditions, hiPSCs differentiate into various neural cell types that self-organize into layered structures resembling specific brain regions such as the forebrain (cerebrum) or midbrain.
Unlike traditional 2D cultures or animal models, 3D brain organoids better preserve cell–cell and cell–matrix interactions, diffusion gradients, and morphological complexity—including diverse populations of neurons, astrocytes, and glial cells. This makes them powerful, human-relevant models for exploring complex neurobiology, modeling neurodevelopmental and neurodegenerative diseases, and accelerating the discovery of new therapeutics.
Recent progress has enabled the culture of brain organoids directly from patient-derived iPSCs or those engineered with disease-relevant mutations using CRISPR technology. As a result, researchers can study cortical development, investigate disease mechanisms, and test compounds for both efficacy and toxicity in systems that more closely reflect human brain biology. While challenges remain in scaling these models for functional genomics, advances in automation, high-content imaging, and AI-driven analysis are rapidly expanding their potential in drug discovery and translational neuroscience.
Brain organoid applications in disease modeling, drug discovery and toxicology
Brain organoids are providing unprecedented insight into human brain biology, offering physiologically relevant models for neurodegenerative, genetic, and injury-related disorders. Molecular Devices’ automated brain organoid systems enable reproducible, long-term culture of 3D neural tissues, combining precise liquid handling, high-content imaging, and AI-driven analysis to support complex experimental designs.
- Alzheimer’s disease – iPSC-derived organoids recapitulate amyloid-beta aggregation and tau pathology. Automation allows high-resolution monitoring of network dynamics, including calcium oscillations, enabling functional assessment of therapeutic candidates (Technology Networks).
- Parkinson’s disease – Midbrain organoids model dopaminergic neuron degeneration. Automated culture and longitudinal imaging provide quantitative insights into neuronal survival and network function, supporting compound screening and mechanistic studies (Biocompare).
- Genetic disorders – Patient-derived or CRISPR-edited organoids, such as Rett syndrome models, exhibit altered neuronal activity. High-throughput, AI-enabled analysis captures subtle electrophysiological and network phenotypes across large cohorts.
- Traumatic brain injury – Organoids replicate injury-induced structural and functional changes. Integrated automation enables dynamic tracking of neural responses, facilitating evaluation of reparative therapies.
- Neurotoxicity and developmental neurotoxicity: Organoids can recapitulate the effects of compounds on the brain, providing insight into the potentially toxic effect of such substances. This is essential for developing safe medications and understanding the consequences of exposure to toxic chemicals.
Molecular Devices’ platforms streamline the production of uniform, assay-ready organoids, improving reproducibility, and reducing manual variability. Researchers can use these systems to detect neurotoxicity early, evaluate compound efficacy, and study disease mechanisms in a human-relevant context, accelerating preclinical discovery and translational research.
Automated workflow for hiPSC-derived brain organoids: From cell culture to functional assays
Researchers typically follow protocols inspired by Lancaster & Knoblich, 2014 or Pasca, 2018, refined for scalability and reproducibility. However, manual brain organoid culture is labor-intensive, variable, and susceptible to contamination, limiting throughput and consistency. Automation addresses these challenges by providing precise, reproducible feeding, handling, and monitoring, improving data quality while freeing scientists to focus on discovery rather than routine maintenance.
At Molecular Devices, we extend these capabilities with an end-to-end automated brain organoid research ecosystem, designed to deliver reproducible, scalable, and standardized culture and evaluation workflows:
- CellXpress.ai® Automated Cell Culture System with rocking incubator enables long-term cultivation of brain organoids with continuous nutrient delivery and minimal variability. This system supports weeks of automated culture, freeing researchers from repetitive tasks and enabling large-scale studies with standardized conditions.
- ImageXpress® HCS.ai High-Content Screening System captures high-resolution morphological and functional data across entire organoids, supporting quantitative assessment of development, disease phenotypes, and therapeutic responses.
- IN Carta® Image Analysis Software applies AI-driven segmentation and phenotypic analysis to extract actionable insights, enabling researchers to track organoid growth, monitor disease progression, and detect subtle drug-induced effects with high precision.
- FLIPR® Penta High-Throughput Cellular Screening System provides functional readouts of neuronal network activity through calcium oscillation assays, delivering critical efficacy and safety endpoints for translational studies.
Together, these technologies form a fully integrated, automated brain organoid workflow, from culture to functional and morphological assessment. By combining automation, high-content imaging, AI-driven analysis, and functional readouts, Molecular Devices enables researchers to accelerate drug discovery, increase experimental reproducibility, and gain deeper insights into human brain biology.
brain organoid cell culture workflow
hiPSC-to-brain organoid cell culture workflow steps
Steps 1–4: iPSC Plating, Media Exchange, Monitoring, and Passaging
Human induced pluripotent stem cells (hiPSCs) are plated and expanded under optimized conditions, with automated imaging used to continuously monitor morphology and cell health. Cell seeding can be automated on a liquid handler—whether for 2D cultures or for organoids embedded in Matrigel—ensuring precision and consistency. Cells are maintained in an incubator, with media exchanges scheduled and executed directly on the liquid handling deck. AI-enabled image analysis provides real-time feedback, allowing the system to trigger downstream steps based on cell status. When cultures reach confluence, automated decision-making protocols initiate passaging, maintaining consistent quality and reproducibility across each stage of the workflow.
Step 5: iPSC Harvesting and Replating
Differentiated iPSCs are harvested and replated into appropriate culture formats. Automation ensures precision and consistency across multiple plates, reducing variability introduced by manual handling.
Step 6: Neural Induction and Organoid Formation
Cells are fed with specific growth factors and neural induction media to initiate organoid formation. Daily imaging with ImageXpress HCS.ai system monitors growth and morphology, while IN Carta AI analysis software quantifies developmental milestones.
Step 7: Organoid Transfer to Six-Well Plates
Organoids are transitioned to larger culture wells – from 96w U-bottom plate to 6w plate – allowing further expansion and maturation.
Step 8: Organoid Differentiation and Maturation
Organoids undergo long-term culture, continuing to differentiate into multiple neuronal and glial cell types. Imaging and AI analysis track structural organization and viability, with maturation often requiring more than 100 days. Here, the rocking incubator provides continuous gentle motion—delivering nutrients and oxygen evenly while preventing aggregation and necrosis.
Step 9: Compound Treatment and Functional Evaluation
Mature organoids are exposed to test compounds to evaluate efficacy and safety. High-content imaging with the ImageXpress Confocal HCS.ai system captures detailed morphological changes, while the FLIPR Penta system measures network-level neuronal activity. Advanced analysis in IN Carta software quantifies calcium oscillations and key parameters such as frequency, amplitude, and synchrony of neuronal firing—providing a comprehensive view of organoid response.
Featured asset
Automated, robust brain organoid generation
Discover how the CellXpress.ai® Automated Cell Culture System streamlines the complex, months-long process of brain organoid generation from iPSCs. This poster highlights a fully automated workflow that minimizes variability and manual handling through optimized liquid handling, integrated media agitation, and on-deck reagent storage. With continuous monitoring and smart scheduling, the system ensures consistent, high-quality organoid development— empowering researchers to scale up brain model production for disease modeling, neurotoxicity testing, and drug discovery with greater confidence and efficiency.
Automated development of iPSC-derived 3D neural organoids and functional analysis of calcium oscillation activity
The CellXpress.ai® Automated Cell Culture System simplifies the development of iPSC-derived 3D neural organoids by automating key steps like media exchanges and imaging. This hands-free workflow enhances reproducibility and scalability, making it ideal for long-term culture and high-throughput applications.
Combined with the FLIPR® Penta system for calcium oscillation analysis and the ImageXpress HCS.ai system for high-content imaging, researchers can assess both functional and morphological maturity of organoids with precision. Discover how this integrated solution accelerates compound screening—download the full poster to learn more.
Latest resources on brain organoid research
The complexity of 3D assays remains a hurdle for the wider adoption of organoid models in research and drug screening. New advanced tools for imaging and analysis, as well as assay automation are critical for increased quality of information, throughput, and precision of complex biological models. Learn how high-throughput, high-content imaging and analysis paired with AI-based analytic tools can improve the accuracy of your brain organoid studies.