organoids.app

Stem cells that build tissue on their own

An organoid is a three-dimensional structure grown in culture from stem cells that organise themselves into something with part of an organ’s architecture and function.6 The FDA’s 2025 roadmap puts it plainly: organoids are “self-organizing cell cultures (e.g. liver organoids, gut organoids) that model native tissue architecture and function”.14 The founding paper is from 2009. Toshiro Sato, Hans Clevers and colleagues at the Hubrecht Institute showed that a single Lgr5-positive stem cell from the mouse intestine, placed in a gel with the right growth factors, builds a crypt-villus structure containing every differentiated cell type of the gut lining, with no supporting tissue around it.1

Two years later a RIKEN group in Kobe reported embryonic stem cells forming an optic cup, the beginning of a retina, through an intrinsic self-organising programme.4 In 2013 Madeline Lancaster and colleagues in Vienna described cerebral organoids with distinct brain regions and used them to model microcephaly,2 and Takanori Takebe’s team in Yokohama grew liver buds from human iPS cells that connected to a host blood supply within 48 hours of transplantation.3 Organoids can start from the adult stem cells of a tissue or from pluripotent stem cells steered by longer differentiation protocols; either way the cells arrange themselves.6

The main organoid types and what each models

• Intestinal organoids. Crypt-villus units from adult stem cells; gut biology, cystic fibrosis and colorectal cancer research.179
• Cerebral organoids. Cortex-like regions with progenitor zones; human brain development and disorders such as microcephaly.2
• Liver organoids and liver buds. Hepatic cells that self-organise with endothelial and mesenchymal cells and carry out liver-specific functions, including human-specific drug metabolism.3
• Kidney organoids. Nephrons with proximal and distal tubules, early loops of Henle and glomeruli; their tubules respond to a nephrotoxicant, which points to nephrotoxicity screening.5
• Retinal organoids. Stratified neural retina from a self-organising optic cup.4
• Tumour organoids. Grown from a patient’s cancer tissue, they keep several properties of the original tumour, including its mutations.9

Patient-derived organoids and living biobanks

Because adult-stem-cell organoids keep the identity of the tissue they came from, organoids grown from a patient’s own cells carry that patient’s genotype. The classic demonstration is cystic fibrosis. In 2013 a Utrecht team showed that intestinal organoids swell when the CFTR channel works and swell far less when it does not, a simple functional readout of the disease-causing defect.7 In 2016 the same group measured responses to CFTR-modulating drugs in rectal organoids from people with a wide range of CFTR mutations and reported that the in vitro responses correlated with published clinical-trial outcomes.8 In cancer, a 2015 Cell paper described a “living biobank” of tumour organoids from twenty consecutive colorectal cancer patients, suitable for high-throughput drug screens,9 and a 2018 Science paper reported that organoids from metastatic gastrointestinal cancers recapitulated the treatment responses of the patients they came from.10 Hubrecht Organoid Technology, a 2013 spin-off of the Hubrecht Institute, KNAW and UMC Utrecht, and a separate foundation biobank in Utrecht now hold collections of patient-derived organoids with sequencing data attached.1112

The regulatory shift toward human-based models

United States drug law used to speak of “preclinical tests (including tests on animals)”. The FDA Modernization Act 2.0, signed on 29 December 2022, replaced that phrase with “nonclinical tests”, a defined term whose list includes cell-based assays, organ chips and microphysiological systems, computer modelling and animal tests.13 Organoids are not named in the statute; the FDA’s April 2025 roadmap for reducing animal testing in preclinical safety studies groups them with organs-on-chips as “in vitro human-derived systems” among the new approach methodologies it intends to validate, starting with monoclonal antibodies.14 On 29 April 2025 the NIH announced an initiative to prioritise human-based research technologies, listing “organoids, tissue chips, and other in vitro systems” first and creating an Office of Research Innovation, Validation, and Application to coordinate it;15 on 10 July 2025 it added that new funding opportunities involving animal models must also support human-focused approaches such as new approach methods.16 The NIH Common Fund’s Complement-ARIE program, approved in January 2024, funds the development, standardisation and validation of those methods.17

Where an organoids app fits: images, screens, records

Organoid work produces images faster than people can measure them, so most organoid software starts at the microscope. OrganoID (2022) recognises, labels and tracks single organoids pixel by pixel in brightfield and phase-contrast images and reports count, size, circularity and other shape metrics over time;18 OrgaQuant (2019) locates and sizes human intestinal organoids with a convolutional network, and its authors released the annotated dataset and trained model;19 OrganoidTracker (2020) follows individual nuclei through time-lapse movies of organoids;20 and OrgaSegment (2024) segments cystic fibrosis organoids to quantify swelling in drug-response assays.21 Underneath sit general open-source tools that organoid labs adapt: Cellpose for segmentation22 and CellProfiler for measurement pipelines.23

At scale, organoids meet high-content screening. A 2020 Nature study built multivariate phenotypic profiles for hundreds of thousands of intestinal organoids in an image-based compound screen,24 and an EPFL group cultured thousands of organoids in microcavity arrays with real-time analysis and screened patient-derived colorectal cancer organoids, noting that a “lack of standardization and quality control” is what keeps organoids from routine industrial use.25 Around the images comes the record-keeping: passages, media changes, line provenance, consent and protocols. Open protocol repositories cover the last item,26 but the culture-tracking layer for organoid labs is still largely built in-house, and that is the gap a product at Organoids.app could name.

Reproducibility and standards

Variability between organoids is the field’s main technical complaint, and the answer is arriving as shared definitions and reference data. A 2021 Cell Stem Cell consensus paper set out an agreed classification, nomenclature and benchmarking guidelines for liver, pancreas and bile-duct organoids,27 and a 2022 Nature Reviews Methods Primer lays out general standards for data quality, reproducibility and deposition.6 The Organoid Cell Atlas, launched as a biological network within the Human Cell Atlas, profiles organoids at single-cell resolution and links them to matching primary tissue, with quality standards for cell composition and cell state as a stated aim;28 its Horizon 2020 pilot, HCA|Organoid, ran from January 2020 to September 2022 with a hundred colon and a hundred brain organoid lines.29 Every one of these efforts produces data and quality metrics that need software to hold them.

Who buys a name like Organoids.app

Who builds around organoids is a fair picture of who might want the name:

• Organoid image-analysis and high-content-screening software teams, whose products already carry names of exactly this shape.1819
• Contract research laboratories offering organoid-based screening and toxicology, now a named category of nonclinical test in United States law.13
• Biobanks and organoid-line catalogues that need a sample-request and provenance portal.12
• Stem-cell reagent, matrix and instrument suppliers wanting a companion app for their consumables and imagers.25
• Consortia, atlases and training programmes that publish protocols, datasets and courses.2628

Organoids app, organoid software, organoid platform

Papers say organoid image analysis, organoid segmentation or organoid tracking. In the lab it is simply the organoids app. Whatever the product is called, the extension sets the expectation: .app sits on the HSTS preload list, so every .app site is HTTPS-only by design.30 Organoids.app is the plural the field uses, on the extension built for software.

1. Sato T et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.Nature, 2009
2. Lancaster MA et al. Cerebral organoids model human brain development and microcephaly.Nature, 2013
3. Takebe T et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant.Nature, 2013
4. Eiraku M et al. Self-organizing optic-cup morphogenesis in three-dimensional culture.Nature, 2011
5. Takasato M et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis.Nature, 2015
6. Zhao Z et al. Organoids.Nature Reviews Methods Primers, 2022
7. Dekkers JF et al. A functional CFTR assay using primary cystic fibrosis intestinal organoids.Nature Medicine, 2013
8. Dekkers JF et al. Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis.Science Translational Medicine, 2016
9. van de Wetering M et al. Prospective derivation of a living organoid biobank of colorectal cancer patients.Cell, 2015
10. Vlachogiannis G et al. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers.Science, 2018
11. Spin-offs: HUB Organoids, established in 2013.Hubrecht Institute
12. Foundation Hubrecht Organoid Biobank.Patient-derived organoid collection, Utrecht
13. Consolidated Appropriations Act, 2023, Public Law 117-328, Section 3209 (Animal testing alternatives): the FDA Modernization Act 2.0.Approved 29 December 2022; 136 Stat. 5821-5822
14. Roadmap to Reducing Animal Testing in Preclinical Safety Studies.U.S. Food and Drug Administration, April 2025
15. NIH to prioritize human-based research technologies.National Institutes of Health, news release, 29 April 2025
16. NIH Funding Announcements to Align with NIH Initiative to Prioritize Human-based Research.NIH Extramural Nexus, 10 July 2025
17. Complement Animal Research In Experimentation (Complement-ARIE).NIH Common Fund
18. Matthews JM et al. OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics.PLoS Computational Biology, 2022
19. Kassis T et al. OrgaQuant: Human intestinal organoid localization and quantification using deep convolutional neural networks.Scientific Reports, 2019
20. Kok RNU et al. OrganoidTracker: Efficient cell tracking using machine learning and manual error correction.PLoS ONE, 2020
21. Lefferts JW et al. OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion.Communications Biology, 2024
22. Stringer C et al. Cellpose: a generalist algorithm for cellular segmentation.Nature Methods, 2021
23. Stirling DR et al. CellProfiler 4: improvements in speed, utility and usability.BMC Bioinformatics, 2021
24. Lukonin I et al. Phenotypic landscape of intestinal organoid regeneration.Nature, 2020
25. Brandenberg N et al. High-throughput automated organoid culture via stem-cell aggregation in microcavity arrays.Nature Biomedical Engineering, 2020
26. Teytelman L et al. Protocols.io: Virtual communities for protocol development and discussion.PLoS Biology, 2016
27. Marsee A et al. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids.Cell Stem Cell, 2021
28. Bock C et al. The Organoid Cell Atlas.Nature Biotechnology, 2021
29. HCA|Organoid: pilot action to establish a multi-tissue human organoid platform within the Human Cell Atlas.CORDIS, European Commission, Horizon 2020 project 874769
30. .app: HTTPS required on all connections through the HSTS preload list.Google Registry