CNS-3D Technology

Human iPSC-Derived CNS-3D Organoids for Predictive, Functional Neurobiology

Reproducible 3D brain organoids derived from human iPSCs capture the complexity of cortical tissue, enabling functional assays to measure neurotoxicity, disease phenotypes, and therapeutic responses across diverse modalities, including small molecules, siRNAs, antisense oligonucleotides, adeno-associated viruses, and antibody-based therapies.

A Complex in vitro Model

CNS-3D Organoids
Cell Types
Reproducibility
Quality Control
Assays
3D Organoids
CNS-3D Organoids are derived from donor-induced pluripotent stem cells (iPSCs) differentiated into neural progenitor cells (NPCs). The resulting structures grow to 500–800 µm in diameter, exhibit spontaneous, electrically driven network activity, and display transcriptomic profiles consistent with human cortical development

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Cell Types
CNS-3D Organoids are comprised of ~50% neurons and ~50% astrocytes which result from the co-differentiation of a single neural progenitor cell suspension. Of this neuron population, 95% are glutamatergic (excitatory) neurons and ~5% are GABAergic (inhibitory) neurons. SnRNAseq analysis confirms that CNS-3D Organoids exhibit a mature biological profile, characterized by a large supporting astrocyte population and a small progenitor cell population.
Key Benefits
FUNCTIONAL
ANALYSIS
Measure actual nerve conduction changes, providing insights beyond simple cell viability assessments.
CLINICALLY RELEVANT 
METRICS
Capture electrophysiological markers used in clinical neuropathy diagnosis, enhancing translation to human outcomes.
DOSE-RESPONSE
CHARACTERIZATION
Establishes clear safety margins for peripheral nerve effects across multiple concentration ranges.
LONGITUDINAL
ASSESSMENT
Track the development of neuropathy over extended exposure periods, revealing cumulative effects that acute studies might miss.
INTEGRATED
EVALUATION
Five distinct functional metrics combine into a Velocity Density Index (VDI), enabling straightforward compound ranking and comparison.
Reproducibility
Consistent and stable organoid pharmacology enables reliable, reproducible results from the first experiment, supports longitudinal (weeks-long) treatment paradigms, and maintains data quality across a validated 4-week assay window.
Quality Control
Each shipment includes a certificate of analysis detailing organoid quality, including brightfield imaging to confirm size consistency (500–800 µm, <5% CV, 98% presence), neuron-to-astrocyte ratios via ICC, sterility (mycoplasma, bacterial, fungal), and assay performance metrics such as EC/IC₅₀and robust Z’ values for FLIPR screening.
Assays
FLIPR Functional Modulation
CNS-3D Organoids exhibit spontaneous functional activity quantifiable via high-throughput FLIPR using a calcium-sensitive fluorophore. Consistent oscillatory waveforms across replicates enable reliable neurotoxicity and neuromodulation screening with as few as four replicates per condition.
Cell Viability Assessment
Cell viability assays like CellTiter-Glo and LDH-Glo can be run alone to reveal dose-dependent effects on organoid health or multiplexed with FLIPR to differentiate neuromodulation from toxicity-driven functional changes.
3D High-content Imaging
High-resolution imaging with custom analysis algorithms enables precise quantification of treatment-induced morphological changes in specific brain cell types at cellular, subcellular, and projection levels.
Multiplexed Sample Collection
Post-treatment CNS-3D Organoids and media can be frozen to preserve RNA, proteins, and secreted factors for downstream analyses, including transcriptomics, proteomics, and ELISA-based biomarker assays.
Additional Assays
CNS-3D Organoids support standard fluorescent, luminescent, and colorimetric assays, including JC-10 for mitochondrial health, Live/Dead imaging for cell-type-specific toxicity, cytokine profiling, and enzymatic activity (e.g., AChE).
Use Case 01

Neurotoxicity

A study published in ALTEX found that CNS-3D Organoids were 7.41 times more accurate than traditional animal models at predicting clinical neurotoxicity because they contain multiple iPSC-derived neural cell types that capture the complexity of human brain tissue. Unlike basic cell cultures, CNS-3D Organoids measure functional electrical activity, enabling detection of early changes in neural network behavior that may indicate toxicity before structural damage occurs.
View Publication
Dose response data of 8 representative compounds with various degrees of toxicity as assessed by potency of neuromodulation (peak count) relative to clinically relevant concentrations (Cmax).
Use Case 02

Disease Modeling

CNS-3D Organoids have been used to model two rare, X-linked neurodevelopmental disorders – Rett Syndrome (RTT) and CDKL5 Deficiency Disorder (CDD). Though these two distinct disorders exhibit overlapping phenotypic features including cognitive deficits, developmental delays, and seizures, when modeled using CNS-3D Organoids we observe striking differences in each disease model in terms of their spontaneous calcium bursting activity profiles.
View Poster
CNS-3D organoids modeling two distinct neurodevelopmental disorders Rett Syndrome (orange) and CDKL5 Deficiency Disorder (teal) display unique functional phenotypes and can be grown in 384-well plate formats.
Use Case 03

Combined Safety & Efficacy Assessment

CNS-3D Organoids derived from healthy control and CDKL5 Deficiency Disorder (CDD) patients were used to identify novel disease-modifying therapeutics. Leveraging a custom brightfield imaging-based predicted toxicity algorithm, we simultaneously assessed compound safety and efficacy—enabling selection of candidates that selectively rescued the CDD FLIPR phenotype without impacting viability or healthy control organoid function.
View Poster
Dose response data demonstrating disease-selective rescue without impacts to cell viability (predicted CTG). Compound restores aberrant CDD organoid function (teal) to Control levels (white).
Use Case 04

Neuromodulator Profiling

Using FLIPR and CTG assays, a study performed in 2019 (Sirenko, 2019 Toxicology) showed that the organoids could detect subtle, dose-dependent effects of known pharmaceuticals, environmental pesticides, industrial compounds and more on neuronal network activity; identifying functional changes prior to overt cytotoxicity. The results highlight the organoids utility for early-stage safety screening, profiling the effects of compounds on neuromodulator-regulated network dynamics and mechanism-of-action studies in CNS drug development.
View Poster
CNS-3D organoids treated with nine  representative compounds cause unique functional phenotypes to appear in fluorescence over time calcium imaging experiments.

Products & Services

CNS-3D Organoids
Designed for high-throughput screening, CNS-3D Organoids are assay ready and available in 96- and 384-well plate formats.
CNS-3D Organoid Standard Services
Turnkey solution for high-throughput neurotoxicity, drug screening, and functional assessments without the need for in-house expertise or infrastructure.
CNS-3D Organoid Custom Services
3D neural models with additional cell types, including microglia for neuroinflammation studies and oligodendrocytes for remyelination and demyelination disorder research.

CNS-3D Technology Resources

Protocol
6/5/2025
CNS-3D Organoids 96-Well Plate
Protocol
6/5/2025
CNS-3D Organoids 384-Well Plate
Protocol
6/5/2025
CNS-3D Organoids FLIPR Assay
Product Sheet
6/5/2025
CNS-3D Organoids
Application Note
6/5/2025
Modeling CDKL5 Deficiency Disorder with CNS-3D Organoids for Streamlined Target Discovery
Publication
10/18/2022
Assessment of a 3D Neural Spheroid Model to Detect Pharmaceutical-Induced Neurotoxicity
Publication
10/22/2020
Screening for Modulators of Neural Network Activity in 3D Human iPSC-Derived Cortical Spheroids
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