Large submaxillary gland cancer tumours, processed with expansion microscopy and visualised on the lightfield4D and analysed with ZEISS arivis Pro. — Sample courtesy of Aroshini Nugawela, Department of Biomedical and Life Sciences, Lancaster University, UK.

3D Organoid Analysis

Accelerate 3D Organoid Drug Discovery with AI-Powered Analysis From imaging to insights in hours, not weeks.

Train custom AI segmentation models in clicks
Build flexible analysis pipelines for any organoid type
Scale from single samples to enterprise screens seamlessly

Complex 3D Models Demand Smarter Analysis

Dense organoids scatter light and hide cellular detail, making image analysis a challenge. Manual segmentation takes days for a single plate, and traditional tools can't handle terabytes of 3D data. AI-powered segmentation and streamlined, scalable image analysis reveal individual cells and even subcellular details in dense 3D structures enabling the multiscale quantification which biological complexity requires. Learn how ZEISS arivis software helps you to make the most of your 3D imaging experiments.

The Complete Workflow for 3D Organoid Analysis From Question to Insight

Train custom AI models easily without code with ZEISS arivis Cloud

What used to require a data scientist and weeks of work, now takes a biologist just one afternoon.

Simply click on objects to train deep learning models
No manual annotation required (but adjustments are possible)
No data science expertise or codng knowledge needed
Cloud-powered training completes in hours
Import to arivis Pro to deploy instantly for your entire dataset

Welplate of organoid samples with enlarged image of organoid 3D analysis results from ZEISS arivis Pro

Build flexible pipelines that answer questions with ZEISS arivis Pro

Complete 3D analysis of large organoid datasets, from raw images to biological insights faster than ever.

Automated AI-powered segmentation with built-in Cellpose or custom Cloud models
Extract hundreds of morphological, intensity, and spatial features
Interactive 3D visualization with immediate feedback
Validate on sample subsets before scaling to full datasets
Analyze multiwell plate data with preserved metadata

Screenshot of ZEISS arivis Hub showcasing scallable analysis or organoids

Scale up analysis to enterprise throughput with ZEISS arivis Hub

Process 96-well plates automatically while you focus on the next experiment.

Deploy validated pipelines from ZEISS arivis Pro at scale
Parallel processing across local servers or cloud infrastructure
Centralized data management with version control
Automated workflows process new data as it arrives
Complete 96-well plate analysis in hours, not days

Your Microscope. Your Data. Our Analysis Software.

ZEISS arivis supports diverse file formats.

No matter what equipment you use to generate your images, ZEISS arivis software is able to process and analysis your datasets.

Try ZEISS arivis Pro

Accelerate Time to Reliable, Reproducible Results Learn how ZEISS arivis software can help you get results faster in various use cases and applications.

Pictogram representing organoid image analysis results — This image is created with Generative AI.

Cancer Organoid Screening

Quantify drug response in patient-derived tumor organoids across dose ranges. Track growth inhibition, cell death, and marker expression changes.

Disease Modeling

Analyze organoid differentiation, lumen formation, and tissue patterning to understand developmental disorders and test therapeutic interventions.

Pictogram representative toxicity and safety assessment results — This image is created with Generative AI.

Toxicity Assessment

Screen compound libraries against hepatic spheroids to predict drug-induced liver injury before clinical trials.

Research Use Only: ZEISS arivis software products are intended for Research and Development only. Quantification of drug response in patient-derived models is for exploratory research and drug discovery purposes only. ZEISS arivis software products are not intended for use in diagnostic procedures, clinical applications, or for the purpose of making clinical decisions for individual patients.

Request a trial

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If you want to have more information on data processing at ZEISS please refer to our data privacy notice