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3D preview of analysis results in which individual cells in the outer layer of an organoid are visualized in different colors.
IMAGE ANALYSIS

AI-Driven Image Analysis for Organoid Research and Analysis

With the FDA’s Modernization Act 2.0, organoids are taking center stage in vital research applications. In life sciences, biotech and pharma labs scientists are eager to adopt AI-driven approaches that will enable complex analysis of organoid growth, volume and quantification in 3D. Our innovative algorithms support your organoid research. From visualization to automated analysis and subcellular segmentation, we’ve got you covered. AI models help take your organoid analysis to new levels.

Light microscopy image of an organoid is analyzed in 3D to reveal individual cells and subcellular structures. The organoid is displayed in green. Nuclei in the pouter cell layer are segmented in red, and nuclei in the lumen display in yellow.

3D visualization of an organoid (green), nuclei in the outer cell layer (red) and nuclei in the lumen (yellow).

Cell-level Organoid Growth Analysis

Single-Cells Segmentation Within Organoids in 3D to Quantify Cell Numbers and Marker Expression for Organoid Growth Analysis

Automated analysis is important to quantify the effects of drugs on growth of organoids and differentiation of cells within organoids.

‍This solution can be used to segment organoids, their lumen, and nuclei within the organoids using a combination of AI tools and conventional image analysis steps in ZEISS arivis Pro. Using the nuclei masks, the cell bodies of the individual cells within the outer layer of the organoids are segmented.

‍Having segmented the organoids and the cells within, several readouts are provided such as organoid and lumen volume, roundness of the organoids, and the number of cells per organoid. Furthermore, marker expression can be analyzed on a single-cell level and the percentage of marker-positive cells is reported. This analysis can be performed for individual images or for hundreds of images acquired using multi-well plates. With ZEISS arivis Hub the 3D organoid analysis is scaled up to include many different organoids.

A 3D visualization of organoid analysis results, the outer layer of the organoid id displayed in green and inside it the lumen is displayed in magenta. On the bottom left corner, a graph is displayed, in which volume of whole organoids and lumen is plotted for 9 (nine) different organoids.

3D Visualization of an organoid (green) and lumen (magenta), for volumetric analysis, which is displayed in a stacked column chart.

Organoid Volume Quantification

Analyze the Volume of Organoids and Their Lumen to Quantify Growth and Differentiation

Automated analysis of organoid growth and differentiation is important for toxicity assays, drug screening and quality control protocols.

This solution can be used to quantify the volume of organoids and their lumens if applicable. As a first step, the organoid area and the lumen area are segmented using a trained deep learning network (trained on ZEISS arivis Cloud). This segmentation is then applied to z-stack images of many organoids gathered from multi-well plates.

For each organoid, 3D objects are generated that are used to quantify the organoid and lumen volumes. Finally, the measurements are presented as tables and interactive plots making it easy to understand and interpret the results.

Based on total volume, organoid growth was assessed. Based on the ratio of lumen per organoid, the differentiation of each individual organoid was assessed.

A screenshot from a webinar about organoid analysis. On the top left you see an organoid microscopy image slice of an organoid, then prediction of an AI model applied to that image on its right. Further right you see a 3D visualization of the entire organoid and on the left a stacked bar plotting organoid and lumen volume of a few organoids. Below the images you see the title of the webinar. The ZEISS logo and the presenter’s face, Dr. Sandra Lemke, are on the bottom left.

Organoid Image Analysis with the Power of AI to Boost Your Research

Recorded Webinar

In this webinar, our expert Dr. Sandra Lemke showcases how organoid images can be analyzed in 2D and 3D using the power of AI without the need to code. We will demonstrate an end-to-end pipeline setup that ensures reproducible results, which help you monitor organoid growth and differentiation.

Further Applications

3D preview of analysis results in which individual cells in the outer layer of an organoid are visualized in different colors.
16 September 2024

Image Analysis Examples for Organoid Growth Analysis

Applications Hub - 10 min read
ZEISS Microscopy
Nuclei and micronuclei segmented in an embryo, on the left you see the green, fluorescent raw image and on the right the 3D analysis of sub cellular structures.
18 September 2022

Cell Phenotype Image Analysis for Cancer Research and Cell Biology

Applications Hub - 6 min read
ZEISS Microscopy
Outer cell layer of fly embryo is analyzed in 3D. individual cells are segmented and highlighted in different colors. Cell volume is visualized on the top left half while cell motion tracks are seen at the bottom right half.
18 September 2024

Image Analysis Examples for Developmental Biology

Applications Hub - 8 min read
ZEISS Microscopy

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    * The images shown on this page represent research content. ZEISS explicitly excludes  the possibility of making a diagnosis or recommending treatment for possibly affected  patients  on the basis of  the information generated with an Axioscan 7 slide scanner.