OrganoSeg is an open-source software that integrates segmentation, filtering, and analysis for breast-cancer spheroid and colon and colorectal-cancer organoid morphologies.

Figure 2 in OrganoSeg Scientific Reports publication

The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the spheroïd.

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Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. The clustering is done with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.

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