arivis Scientific Image Analysis

Cell-level Organoid Analysis

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Cell-level Organoid Analysis


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Before and After Analysis

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Solution Description

Automated analysis is important to quantify the effects of drugs on growth of organoids and differentiation of cells with 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 arivis Vision4D. 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, a number of 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.



Figure 1: 3D visualization of an organoid (green), nuclei in the outer cell layer (red) and nuclei in the lumen (yellow).

arivis Vision4D, arivis VisionHub, Celldiscoverer 7, organoid, growth, differentiation, marker expression, single-cell level analysis, nuclei counting
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