April 16, 2026

Flex Tech

Innovation in Every Curve

From organoid culture to manufacturing: technologies for reproducible and scalable organoid production

From organoid culture to manufacturing: technologies for reproducible and scalable organoid production
  • Lancaster, M. A. & Knoblich, J. A. Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345, 1247125 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Birtele, M., Lancaster, M. & Quadrato, G. Modelling human brain development and disease with organoids. Nat. Rev. Mol. Cell Biol. 26, 389–412 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Verstegen, M. M. A. et al. Clinical applications of human organoids. Nat. Med. 31, 409–421 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yao, Q. et al. Organoids: development and applications in disease models, drug discovery, precision medicine, and regenerative medicine. MedComm 5, e735 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rossi, G., Manfrin, A. & Lutolf, M. P. Progress and potential in organoid research. Nat. Rev. Genet. 19, 671–687 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zushin, P.-J. H., Mukherjee, S. & Wu, J. C. FDA Modernization Act 2.0: transitioning beyond animal models with human cells, organoids, and AI/ML-based approaches. J. Clin Investig. 133 (2023).

  • Tagle, D. A. The NIH microphysiological systems program: developing in vitro tools for safety and efficacy in drug development. Curr. Opin. Pharmacol. 48, 146–154 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhou, L. et al. Organoids and organs-on-chips: recent advances, applications in drug development, and regulatory challenges. Med 6 (2025).

  • Ahn, S.-J. et al. Essential guidelines for manufacturing and application of organoids. Int. J. Stem Cells 17, 102–112 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lee, H., Im, J. S., Choi, D. B. & Woo, D.-H. Trends in the global organoid technology and industry: from organogenesis in a dish to the commercialization of organoids. Organoid 1, e11 (2021).

    Article 

    Google Scholar 

  • Homan, K. A. Industry adoption of organoids and organs-on-chip technology: toward a paradox of choice. Adv. Biol. 7, 2200334 (2023).

    Article 
    CAS 

    Google Scholar 

  • Hofer, M. & Lutolf, M. P. Engineering organoids. Nat. Rev. Mater. 6, 402–420 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Heinzelmann, E. et al. iPSC-derived and patient-derived organoids: applications and challenges in scalability and reproducibility as pre-clinical models. Curr. Res. Toxicol. 7, 100197 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yin, X. et al. Engineering stem cell organoids. Cell Stem Cell 18, 25–38 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brassard, J. A. & Lutolf, M. P. Engineering stem cell self-organization to build better organoids. Cell Stem Cell 24, 860–876 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Blatchley, M. R. & Anseth, K. S. Middle-out methods for spatiotemporal tissue engineering of organoids. Nat. Rev. Bioeng. 1, 329–345 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gaspar, V. M., Lavrador, P., Borges, J., Oliveira, M. B. & Mano, J. F. Advanced bottom-up engineering of living architectures. Adv. Mater. 32, 1903975 (2020).

    Article 
    CAS 

    Google Scholar 

  • Velasco, V., Shariati, S. A. & Esfandyarpour, R. Microtechnology-based methods for organoid models. Microsyst. Nanoeng. 6, 76 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • OECD. Guidance document on good in vitro method practices (GIVIMP) OECD Ser. Test. Assess, 286 (2018).

  • Ahn, S.-J. Standards for organoids. Int. J. Stem Cells 17, 99–101 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lee, H. et al. Standardization and quality assessment for human intestinal organoids. Front. Cell Dev. Biol. 12, 1383893 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Garreta, E. et al. Rethinking organoid technology through bioengineering. Nat. Mater. 20, 145–155 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Takebe, T., Zhang, B. & Radisic, M. Synergistic engineering: organoids meet organs-on-a-chip. Cell Stem Cell 21, 297–300 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, S., Wan, Z. & Kamm, R. D. Vascularized organoids on a chip: strategies for engineering organoids with functional vasculature. Lab Chip 21, 473–488 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Takebe, T. & Wells, J. M. Organoids by design. Science 364, 956–959 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kozlowski, M. T., Crook, C. J. & Ku, H. T. Towards organoid culture without Matrigel. Commun. Biol. 4, 1387 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fang, G., Chen, Y. C., Lu, H. & Jin, D. Advances in spheroids and organoids on a chip. Adv. Funct. Mater. 33, 2215043 (2023).

    Article 
    CAS 

    Google Scholar 

  • Broguiere, N. et al. Growth of epithelial organoids in a defined hydrogel. Adv. Mater. 30, 1801621 (2018).

    Article 

    Google Scholar 

  • Gan, Z., Qin, X., Liu, H., Liu, J. & Qin, J. Recent advances in defined hydrogels in organoid research. Bioact. Mater. 28, 386–401 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, K., He, Y., Jin, X., Jin, K. & Qian, J. Reproducible extracellular matrices for tumor organoid culture: challenges and opportunities. J. Transl. Med. 23, 497 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhang, Y., Qi, F., Chen, P., Liu, B.-F. & Li, Y. Spatially defined microenvironment for engineering organoids. Biophysics Reviews 5 (2024).

  • Velasco, S. et al. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature 570, 523–527 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Broutier, L. et al. Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation. Nat. Protoc. 11, 1724–1743 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Freedman, B. S. et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat. Commun. 6, 8715 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Morizane, R. & Bonventre, J. V. Generation of nephron progenitor cells and kidney organoids from human pluripotent stem cells. Nat. Protoc. 12, 195–207 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hughes, C. S., Postovit, L. M. & Lajoie, G. A. Matrigel: a complex protein mixture required for optimal growth of cell culture. Proteomics 10, 1886–1890 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kratochvil, M. J. et al. Engineered materials for organoid systems. Nat. Rev. Mater. 4, 606–622 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Aisenbrey, E. A. & Murphy, W. L. Synthetic alternatives to Matrigel. Nat. Rev. Mater. 5, 539–551 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sachs, N., Tsukamoto, Y., Kujala, P., Peters, P. J. & Clevers, H. Intestinal epithelial organoids fuse to form self-organizing tubes in floating collagen gels. Development 144, 1107–1112 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sandilya, S. & Singh, S. Development of islet organoids from human induced pluripotent stem cells in a cross-linked collagen scaffold. Cell Regener. 10, 38 (2021).

    Article 
    CAS 

    Google Scholar 

  • Buchmann, B. et al. Mechanical plasticity of collagen directs branch elongation in human mammary gland organoids. Nat. Commun. 12, 2759 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, Y. et al. One-step synthesis of composite hydrogel capsules to support liver organoid generation from hiPSCs. Biomater. Sci. 8, 5476–5488 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, Z. et al. Advances of engineered hydrogel organoids within the stem cell field: a systematic review. Gels 8, 379 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kutikov, A. B. & Song, J. Biodegradable PEG-based amphiphilic block copolymers for tissue engineering applications. Acs Biomater. Sci. Eng. 1, 463–480 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Drumheller, P. D. & Hubbell, J. A. Densely crosslinked polymer networks of poly (ethylene glycol) in trimethylolpropane triacrylate for cell-adhesion-resistant surfaces. J. Biomed. Mater. Res. 29, 207–215 (1995).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cruz-Acuña, R. et al. PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery. Nat. Protoc. 14, 2258–2258 (2019).

    Article 
    PubMed 

    Google Scholar 

  • Salinas, C. N. & Anseth, K. S. Mixed mode thiol-acrylate photopolymerizations for the synthesis of PEG-peptide hydrogels. Macromolecules 41, 6019–6026 (2008).

    Article 
    CAS 

    Google Scholar 

  • Andreopoulos, F. M. et al. Photoscissable hydrogel synthesis via rapid photopolymerization of novel PEG-based polymers in the absence of photoinitiators. J. Am. Chem. Soc. 118, 6235–6240 (1996).

    Article 
    CAS 

    Google Scholar 

  • Lin, C. C., Raza, A. & Shih, H. PEG hydrogels formed by thiol-ene photo-click chemistry and their effect on the formation and recovery of insulin-secreting cell spheroids. Biomaterials 32, 9685–9695 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kim, K. H., Kim, J. & Jo, W. H. Preparation of hydrogel nanoparticles by atom transfer radical polymerization of -isopropylacrylamide in aqueous media using PEG macro-initiator. Polymer 46, 2836–2840 (2005).

    Article 
    CAS 

    Google Scholar 

  • D’souza, A. A. & Shegokar, R. Polyethylene glycol (PEG): a versatile polymer for pharmaceutical applications. Expert Opin. Drug Deliv. 13, 1257–1275 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Salinas, C. N. & Anseth, K. S. The influence of the RGD peptide motif and its contextual presentation in PEG gels on human mesenchymal stem cell viability. J. Tissue Eng. Regener. Med. 2, 296–304 (2008).

    Article 
    CAS 

    Google Scholar 

  • Wang, C., Tong, X. M., Jiang, X. Y. & Yang, F. Effect of matrix metalloproteinase-mediated matrix degradation on glioblastoma cell behavior in 3D PEG-based hydrogels. J. Biomed. Mater. Res. Part A 105, 770–778 (2017).

    Article 
    CAS 

    Google Scholar 

  • Suwannakot, P. et al. Electrostatic assembly of multiarm PEG-based hydrogels as extracellular matrix mimics: cell response in the presence and absence of RGD cell adhesive ligands. Acs Biomater. Sci. Eng. 9, 1362–1376 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cai, L. & Heilshorn, S. C. Designing ECM-mimetic materials using protein engineering. Acta Biomater. 10, 1751–1760 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cruz-Acuña, R. et al. Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Nat. Cell Biol. 19, 1326–1335 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Glorevski, N. et al. Designer matrices for intestinal stem cell and organoid culture. Nature 539, 560–564 (2016).

    Article 

    Google Scholar 

  • Hernandez-Gordillo, V. et al. Fully synthetic matrices for culture of primary human intestinal enteroids and endometrial organoids. Biomaterials 254, 120125 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gjorevski, N. & Lutolf, M. P. Synthesis and characterization of well-defined hydrogel matrices and their application to intestinal stem cell and organoid culture. Nat. Protoc. 12, 2263–2274 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ng, S. S. et al. Human iPS-derived progenitors bioengineered into liver organoids using an inverted colloidal crystal poly (ethylene glycol) scaffold. Biomaterials 182, 299–311 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sorrentino, G. et al. Mechano-modulatory synthetic niches for liver organoid derivation. Nat. Commun. 11, 3416 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Majumder, J. et al. Human-induced pluripotent stem cell-derived planar neural organoids assembled on synthetic hydrogels. J. Tissue Eng. 15, 20417314241230633 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ranga, A. et al. Neural tube morphogenesis in synthetic 3D microenvironments. Proc. Natl. Acad. Sci. USA 113, E6831–E6839 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vallmajo-Martin, Q., Broguiere, N., Millan, C., Zenobi-Wong, M. & Ehrbar, M. PEG/HA hybrid hydrogels for biologically and mechanically tailorable bone marrow organoids. Adv. Funct. Mater. 30, 1910282 (2020).

    Article 
    CAS 

    Google Scholar 

  • Below, C. R. et al. A microenvironment-inspired synthetic three-dimensional model for pancreatic ductal adenocarcinoma organoids. Nat. Mater. 21, 110–119 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zimoch, J. et al. Polyisocyanopeptide hydrogels: A novel thermo-responsive hydrogel supporting pre-vascularization and the development of organotypic structures. Acta Biomater. 70, 129–139 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, B., Shao, J., Jansen, J. A., Walboomers, X. F. & Yang, F. A Novel thermoresponsive gel as a potential delivery system for lipoxin. J. Dent. Res. 98, 355–362 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, K. Z. et al. Structure and applications of PIC-based polymers and hydrogels. Cell Rep. Phys. Sci. 5, 101834 (2024).

  • Ye, S. C., Boeter, J. W. B., Penning, L. C., Spee, B. & Schneeberger, K. Hydrogels for liver tissue engineering. Bioengineering 6, 59 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Prince, E. Designing biomimetic strain-stiffening into synthetic hydrogels. Biomacromolecules 25, 6283–6295 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Xu, J. Y., Jiang, Y. & Gao, L. Synthetic strain-stiffening hydrogels towards mechanical adaptability. J. Mater. Chem. B 11, 221–243 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, Y. et al. Polyisocyanide hydrogels as a tunable platform for mammary gland organoid formation. Adv. Sci. 7, 2001797 (2020).

    Article 
    CAS 

    Google Scholar 

  • Ye, S. C. et al. A chemically defined hydrogel for human liver organoid culture. Adv. Funct. Mater. 30, 2000893 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Baker, B. A., Murff, R. L. & Milam, V. T. Tailoring the mechanical properties of polyacrylamide-based hydrogels. Polymer 51, 2207–2214 (2010).

    Article 
    CAS 

    Google Scholar 

  • Wang, Y. et al. Polyacrylamide-based hydrogel with biocompatibility and tunable stiffness for three-dimensional cell culture. ACS Appl. Biol. Mater. 8, 2356–2364 (2025).

    Article 
    CAS 

    Google Scholar 

  • Milos, F. & del Campo, A. Polyacrylamide hydrogels as versatile biomimetic platforms to study cell-materials interactions. Adv. Mater. Interfaces 11, 2400404 (2024).

    Article 
    CAS 

    Google Scholar 

  • Shkumatov, A., Baek, K. & Kong, H. Matrix rigidity-modulated cardiovascular organoid formation from embryoid bodies. Plos One 9, e94764 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Urushizaki, F. et al. Swelling and mechanical-properties of poly(vinyl alcohol) hydrogels. Int. J. Pharm. 58, 135–142 (1990).

    Article 
    CAS 

    Google Scholar 

  • Jiang, S., Liu, S. & Feng, W. H. PVA hydrogel properties for biomedical application. J. Mech. Behav. Biomed. Mater. 4, 1228–1233 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Qi, X. L. et al. Investigation of Salecan/poly(vinyl alcohol) hydrogels prepared by freeze/thaw method. Carbohydr. Polym. 118, 60–69 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kim, T. H. et al. Creating stiffness gradient polyvinyl alcohol hydrogel using a simple gradual freezing-thawing method to investigate stem cell differentiation behaviors. Biomaterials 40, 51–60 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gupta, A., Kumar, R., Upadhyay, N. K., Surekha, P. & Roy, P. K. Synthesis, characterization and efficacy of chemically crosslinked PVA hydrogels for dermal wound healing in experimental animals. J. Appl. Polym. Sci. 111, 1400–1408 (2009).

    Article 
    CAS 

    Google Scholar 

  • Jiang, X., Li, C. L. & Han, Q. Modulation of swelling of PVA hydrogel by polymer and crosslinking agent concentration. Polym. Bull. 80, 1303–1320 (2023).

    Article 
    CAS 

    Google Scholar 

  • Jung, N., Moreth, T., Stelzer, E. H. K., Pampaloni, F. & Windbergs, M. Non-invasive analysis of pancreas organoids in synthetic hydrogels defines material-cell interactions and luminal composition. Biomater. Sci. 9, 5485–5496 (2021).

    Article 

    Google Scholar 

  • Wiedenmann, S. et al. Single-cell-resolved differentiation of human induced pluripotent stem cells into pancreatic duct-like organoids on a microwell chip. Nat. Biomed. Eng. 5, 897–913 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brandenberg, N. et al. High-throughput automated organoid culture via stem-cell aggregation in microcavity arrays. Nat. Biomed. Eng. 4, 863–874 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kakni, P., Truckenmüller, R., Habibovic, P., van Griensven, M. & Giselbrecht, S. A Microwell-based intestinal organoid-macrophage co-culture system to study intestinal inflammation. Int. J. Mol. Sci. 23, 15364 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Loebel, C. et al. Microstructured hydrogels to guide self-assembly and function of lung alveolospheres. Adv. Mater. 34, 2202992 (2022).

    Article 
    CAS 

    Google Scholar 

  • Chen, C., Rengarajan, V., Kjar, A. & Huang, Y. A matrigel-free method to generate matured human cerebral organoids using 3D-Printed microwell arrays. Bioact. Mater. 6, 1130–1139 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Kakni, P. et al. Intestinal organoid culture in polymer film-based microwell arrays. Adv. Biosyst. 4, 2000126 (2020).

    Article 
    CAS 

    Google Scholar 

  • Kim, D., Lim, H., Youn, J., Park, T. E. & Kim, D. S. Scalable production of uniform and mature organoids in a 3D geometrically-engineered permeable membrane. Nat. Commun. 15, 9420 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tran, T. et al. A scalable organoid model of human autosomal dominant polycystic kidney disease for disease mechanism and drug discovery. Cell Stem Cell 29, 1083–1101 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jiang, S. Q. et al. Development of a high-throughput micropatterned agarose scaffold for consistent and reproducible hPSC-derived liver organoids. Biofabrication 15, 015006 (2023).

    Article 
    CAS 

    Google Scholar 

  • Gjorevski, N. et al. Tissue geometry drives deterministic organoid patterning. Science 375, eaaw9021 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sen, D., Voulgaropoulos, A. & Keung, A. J. Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids. BMC Biotechnol. 21, 59 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karzbrun, E. et al. Human neural tube morphogenesis in vitro by geometric constraints. Nature 599, 268–272 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lavickova, B. et al. Integrated microfluidic platform for high-throughput generation of intestinal organoids in hydrogel droplets. Preprint at (2025).

  • Abbasalizadeh, S. et al. Continuous production of highly functional vascularized hepatobiliary organoids from human pluripotent stem cells using a scalable microfluidic platform. Adv. Funct. Mater. 33, 2210233 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhu, Y. J. et al. Engineering microcapsules to construct vascularized human brain organoids. Chem. Eng. J. 424, 130427 (2021).

    Article 
    CAS 

    Google Scholar 

  • Liu, H. T. et al. A droplet microfluidic system to fabricate hybrid capsules enabling stem cell organoid engineering. Adv. Sci. 7, 1903739 (2020).

    Article 
    CAS 

    Google Scholar 

  • Lee, J.-H. et al. Development of robust antiviral assays using relevant apical-out human airway organoids. Preprint at (2024).

  • Ganguli, A. et al. Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging. Sci. Adv. 7, eabc1323 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhu, Y. J. et al. generation of human brain organoids on a micropillar array. Lab a Chip 17, 2941–2950 (2017).

    Article 
    CAS 

    Google Scholar 

  • Acharya, P. et al. Uniform cerebral organoid culture on a pillar plate by simple and reproducible spheroid transfer from an ultralow attachment well plate. Biofabrication 16, 025005 (2024).

    Article 
    CAS 

    Google Scholar 

  • Wang, Y. Q. et al. differentiation and generation of functional liver organoids from human iPSCs in a 3D perfusable chip system. Lab Chip 18, 3606–3616 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sozzi, E. et al. Silk scaffolding drives self-assembly of functional and mature human brain organoids. Front. Cell Dev. Biol. 10, 1023279 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McMurtrey, R. J. Patterned and functionalized nanofiber scaffolds in three-dimensional hydrogel constructs enhance neurite outgrowth and directional control. J. Neural Eng. 11, 066009 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Giandomenico, S. L., Sutcliffe, M. & Lancaster, M. A. Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development. Nat. Protoc. 16, 579–602 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ritzau-Reid, K. I. et al. Microfibrous scaffolds guide stem cell lumenogenesis and brain organoid engineering. Adv. Mater. 35, 2300305 (2023).

    Article 
    CAS 

    Google Scholar 

  • Yavitt, F. M. et al. In situ modulation of intestinal organoid epithelial curvature through photoinduced viscoelasticity directs crypt morphogenesis. Sci. Adv. 9, eadd5668 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Skylar-Scott, M. A. et al. Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues. Nat. Biomed. Eng. 6, 449–462 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Porter, C. M., Qian, G. C., Grindel, S. H. & Hughes, A. J. Highly parallel production of designer organoids by mosaic patterning of progenitors. Cell Syst. 15, 649–661 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Skylar-Scott, M. A. et al. Biomanufacturing of organ-specific tissues with high cellular density and embedded vascular channels. Sci. Adv. 5, eaaw2459 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wolf, K. J., Weiss, J. D., Uzel, S. G. M., Skylar-Scott, M. A. & Lewis, J. A. Biomanufacturing human tissues via organ building blocks. Cell Stem Cell 29, 667–677 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wilson, Z. E. et al. Inter-individual variability in levels of human microsomal protein and hepatocellularity per gram of liver. Br. J. Clin. Pharmacol. 56, 433–440 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bianconi, E. et al. An estimation of the number of cells in the human body. Ann. Hum. Biol. 40, 463–471 (2013).

    Article 
    PubMed 

    Google Scholar 

  • Tirziu, D., Giordano, F. J. & Simons, M. Cell communications in the heart. Circulation 122, 928–937 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lázár, E., Sadek, H. A. & Bergmann, O. Cardiomyocyte renewal in the human heart: insights from the fall-out. Eur. Heart J. 38, 2333–2339c (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Homan, K. A. et al. Flow-enhanced vascularization and maturation of kidney organoids in vitro. Nat. Methods 16, 255–262 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Decembrini, S., Hoehnel, S., Brandenberg, N., Arsenijevic, Y. & Lutolf, M. P. Hydrogel-based milliwell arrays for standardized and scalable retinal organoid cultures. Sci. Rep. 10, 10275 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Suenaga, R. et al. Microwell bag culture for large-scale production of homogeneous islet-like clusters. Sci. Rep. 12, 5221 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pettinato, G. et al. Spectroscopic label-free microscopy of changes in live cell chromatin and biochemical composition in transplantable organoids. Sci. Adv. 7, eabj2800 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Narazaki, G. et al. Scalable production of human cortical organoids using a biocompatible polymer. Nat. Biomed. Eng. 1–9 (2025).

  • Lee, S. et al. Membrane-bottomed microwell array added to Transwell insert to facilitate non-contact co-culture of spermatogonial stem cell and STO feeder cell. Biofabrication 12, 045031 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Ornoff, D. M., Wang, Y. L., Proctor, A., Shah, A. S. & Allbritton, N. L. Co-fabrication of chitosan and epoxy photoresist to form microwell arrays with permeable hydrogel bottoms. Biomaterials 74, 77–88 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kim, D. et al. A deep and permeable nanofibrous oval-shaped microwell array for the stable formation of viable and functional spheroids. Biofabrication 13, 035050 (2021).

    Article 
    CAS 

    Google Scholar 

  • Jiang, S. W. et al. An automated organoid platform with inter-organoid homogeneity and inter-patient heterogeneity. Cell Rep. Med. 1, 100161 (2020).

  • Zhang, Y. M. et al. A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments. Nat. Commun. 15, 3382 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fang, G. C. et al. Mammary tumor organoid culture in non-adhesive alginate for luminal mechanics and high-throughput drug screening. Adv. Sci. 8, 2102418 (2021).

    Article 
    CAS 

    Google Scholar 

  • Bochenek, M. A. et al. Alginate encapsulation as long-term immune protection of allogeneic pancreatic islet cells transplanted into the omental bursa of macaques. Nat. Biomed. Eng. 2, 810–821 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, H. T. et al. Organoid in droplet: production of uniform pancreatic cancer organoids from single cells. Mater. Today Bio 32, 101765 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhang, W. J. et al. Microfluidic droplets as structural templates for Matrigel to enable 1-week large organoid modeling. Chem. Eng. Sci. 238, 116632 (2021).

    Article 
    CAS 

    Google Scholar 

  • Zhang, W. J. et al. Microfluidic droplet encapsulation-guided organoid growth promotes parental tumor phenotype recapitulation. Int. J. Cancer 154, 145–154 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schindler, M. et al. Agarose microgel culture delineates lumenogenesis in naive and primed human pluripotent stem cells. Stem Cell Rep. 16, 1347–1362 (2021).

    Article 
    CAS 

    Google Scholar 

  • Bavli, D. et al. CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones. Dev. Cell 56, 1804–1817 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, Z. H. et al. Rapid tissue prototyping with micro-organospheres. Stem Cell Rep. 17, 1959–1975 (2022).

    Article 
    CAS 

    Google Scholar 

  • Lee, D. H., Jang, M. & Park, J. K. Rapid one-step purification of single-cells encapsulated in alginate microcapsules from oil to aqueous phase using a hydrophobic filter paper: Implications for single-cell experiments. Biotechnol. J. 9, 1233–1240 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, Y. L. & Hu, J. J. Sub-100-micron calcium-alginate microspheres: Preparation by nitrogen flow focusing, dependence of spherical shape on gas streams and a drug carrier using acetaminophen as a model drug. Carbohydr. Polym. 269, 118262 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Przepiorski, A. et al. A simple bioreactor-based method to generate kidney organoids from pluripotent stem Cells. Stem Cell Rep. 11, 470–484 (2018).

    Article 
    CAS 

    Google Scholar 

  • Schneeberger, K. et al. Large-scale production of LGR5-positive bipotential human liver stem cells. Hepatology 72, 257–270 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • DiStefano, T. et al. Accelerated and improved differentiation of retinal organoids from pluripotent stem cells in rotating-wall vessel bioreactors. Stem Cell Rep. 10, 300–313 (2018).

    Article 
    CAS 

    Google Scholar 

  • Takahashi, J. et al. Suspension culture in a rotating bioreactor for efficient generation of human intestinal organoids. Cell Rep. Methods 2, 100337 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ho, D. L. et al. Large-scale production of wholly cellular bioinks via the optimization of human induced pluripotent stem cell aggregate culture in automated bioreactors. Adv. Healthc. Mater. 11, 2201138 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Borys, B. S. et al. Overcoming bioprocess bottlenecks in the large-scale expansion of high-quality hiPSC aggregates in vertical-wheel stirred suspension bioreactors. Stem Cell Res. Ther. 12, 55 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Palladino, F. et al. Bioreactors: applications and innovations for a sustainable and healthy future-a critical review. Appl. Sci. 14, 9346 (2024).

    Article 
    CAS 

    Google Scholar 

  • Schuster, B. et al. Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids. Nat. Commun. 11, 5271 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Berger, E. et al. Millifluidic culture improves human midbrain organoid vitality and differentiation. Lab Chip 18, 3172–3183 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Czerniecki, S. M. et al. High-throughput screening enhances kidney organoid differentiation from human pluripotent stem cells and enables automated multidimensional phenotyping. Cell Stem Cell 22, 929–940 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Renner, H. et al. A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids. Elife 9, e52904 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tischler, J. et al. An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates. Cell Rep. Methods 2, 100244 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Seiler, S. T. et al. Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids. Sci. Rep. 12, 20173 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Filan, C. et al. Non-invasive label-free imaging analysis pipeline for in situ characterization of 3D brain organoids. Sci. Rep. 14, 22331 (2024).

    Article 
    CAS 

    Google Scholar 

  • Charles, S. et al. Non-invasive quality control of organoid cultures using mesofluidic CSTR bioreactors and high-content imaging. Adv. Mater. Technol. 10, 2400473 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kretzschmar, K. & Clevers, H. Organoids: modeling development and the stem cell niche in a dish. Dev. Cell 38, 590–600 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ayan, B. et al. Aspiration-assisted bioprinting for precise positioning of biologics. Sci. Adv. 6, eaaw5111 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Higa, A. et al. High-throughput in vitro assay using patient-derived tumor organoids. J. Vis. Exp.172, e62668 (2021).

  • Takahashi, N. et al. Construction of in vitro patient-derived tumor models to evaluate anticancer agents and cancer immunotherapy. Oncol. Lett. 21, 406 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kondo, J. et al. High-throughput screening in colorectal cancer tissue-originated spheroids. Cancer Sci. 110, 345–355 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ayan, B., Wu, Y., Karuppagounder, V., Kamal, F. & Ozbolat, I. T. Aspiration-assisted bioprinting of the osteochondral interface. Sci. Rep. 10, 13148 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Grexa, I. et al. SpheroidPicker for automated 3D cell culture manipulation using deep learning. Sci. Rep. 11, 14813 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dornhof, J. et al. Bioprinting-based automated deposition of single cancer cell spheroids into oxygen sensor microelectrode wells. Lab a Chip 22, 4369–4381 (2022).

    Article 
    CAS 

    Google Scholar 

  • Gutzweiler, L. et al. Large scale production and controlled deposition of single HUVEC spheroids for bioprinting applications. Biofabrication 9, 025027 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Mironov, V. et al. Organ printing: tissue spheroids as building blocks. Biomaterials 30, 2164–2174 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stern, A. et al. The CellRaft AIR® system: a novel system enabling organoid imaging, identification, and isolation. Slas Discov. 27, 201–208 (2022).

    Article 
    PubMed 

    Google Scholar 

  • Roth, J. G. et al. Spatially controlled construction of assembloids using bioprinting. Nat. Commun. 14, 4346 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zieger, V. et al. Towards automation in 3D cell culture: selective and gentle high-throughput handling of spheroids and organoids via novel Pick-Flow-Drop principle. Adv. Healthc. Mater. 13, 2303350 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yang, X. et al. Kirigami electronics for long-term electrophysiological recording of human neural organoids and assembloids. Nat. Biotechnol. 42, 1836–1843 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kim, J. -i et al. Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway. Neuron 112, 4048–4059 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lin, M. et al. Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche. Nat. Commun. 14, 3025 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, L. et al. A human three-dimensional neural-perivascular ‘assembloid’ promotes astrocytic development and enables modeling of SARS-CoV-2 neuropathology. Nat. Med. 27, 1600–1606 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hu, Y. W. et al. Lung cancer organoids analyzed on microwell arrays predict drug responses of patients within a week. Nat. Commun. 12, 2581 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Choi, D. et al. Microfluidic organoid cultures derived from pancreatic cancer biopsies for personalized testing of chemotherapy and immunotherapy. Adv. Sci. 11, 2303088 (2024).

    Article 
    CAS 

    Google Scholar 

  • Liu, X. et al. Recent progress on the organoids: techniques, advantages and applications. Biomed. Pharmacother. 185, 117942 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Jin, H. et al. Advancing organoid engineering for tissue regeneration and biofunctional reconstruction. Biomater. Res. 28, 0016 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Arjmand, B. et al. Advancement of organoid technology in regenerative medicine. Regener. Eng. Transl. Med. 9, 83–96 (2023).

    Article 

    Google Scholar 

  • Zhao, Z. et al. Organoids. Nat. Rev. Methods Prim. 2, 94 (2022).

    Article 
    CAS 

    Google Scholar 

  • Rossen, N. S. et al. Injectable therapeutic organoids using sacrificial hydrogels. iScience 23, 101052 (2020).

  • Wang, Y. et al. In situ differentiation and generation of functional liver organoids from human iPSCs in a 3D perfusable chip system. Lab Chip 18, 3606–3616 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nikolaev, M. et al. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585, 574–578 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Brassard, J. A., Nikolaev, M., Hübscher, T., Hofer, M. & Lutolf, M. P. Recapitulating macro-scale tissue self-organization through organoid bioprinting. Nat. Mater. 20, 22–29 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Abilez, O. J. et al. Gastruloids enable modeling of the earliest stages of human cardiac and hepatic vascularization. Science 388, eadu9375 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Volmert, B. et al. A patterned human primitive heart organoid model generated by pluripotent stem cell self-organization. Nat. Commun. 14, 8245 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lewis-Israeli, Y. R. et al. Self-assembling human heart organoids for the modeling of cardiac development and congenital heart disease. Nat. Commun. 12, 5142 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quintard, C. et al. A microfluidic platform integrating functional vascularized organoids-on-chip. Nat. Commun. 15, 1452 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bai, L. et al. AI-enabled organoids: Construction, analysis, and application. Bioact. Mater. 31, 525–548 (2024).

    PubMed 

    Google Scholar 

  • Zhou, L. et al. When artificial intelligence (AI) meets organoids and organs-on-chips (OoCs): game-changer for drug discovery and development. Innov. Life 3, 100115 (2025).

  • Du, X. et al. Organoids revealed: morphological analysis of the profound next generation in-vitro model with artificial intelligence. Bio-Des. Manuf. 6, 319–339 (2023).

    Article 

    Google Scholar 

  • Beghin, A. et al. Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification. Nat. Methods 19, 881–892 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Okamoto, T. et al. Integration of human inspection and artificial intelligence-based morphological typing of patient-derived organoids reveals interpatient heterogeneity of colorectal cancer. Cancer Sci. 113, 2693–2703 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kowalczewski, A. et al. Design optimization of geometrically confined cardiac organoids enabled by machine learning techniques. Cell Rep. Methods 4, 700798 (2024).

  • Kong, J. et al. Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients. Nat. Commun. 11, 5485 (2020).

  • Kassis, T., Hernandez-Gordillo, V., Langer, R. & Griffith, L. G. OrgaQuant: human intestinal organoid localization and quantification using deep convolutional neural networks. Sci. Rep. 9, 12479 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Beghin, A. et al. High content 3D imaging method for quantitative characterization of organoid development and phenotype. Preprint at (2021).

  • Mo, Y. et al. Artificial intelligence for organoids multidimensional assessment. SmartMat 6, e70016 (2025).

    Article 
    CAS 

    Google Scholar 

  • Maramraju, S. et al. AI-organoid integrated systems for biomedical studies and applications. Bioeng. Transl. Med. 9, e10641 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shin, W. & Kim, H. J. 3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert. Nat. Protoc. 17, 910 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karzbrun, E., Kshirsagar, A., Cohen, S. R., Hanna, J. H. & Reiner, O. Human brain organoids on a chip reveal the physics of folding. Nat. Phys. 14, 515 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Youn, J., Kim, D., Kwak, H., Lee, A. & Kim, D. S. Tissue-scale in vitro epithelial wrinkling and wrinkle-to-fold transition. Nat. Commun. 15, 7118 (2024).

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