Tutorials

SMURF relies on external packages for nuclei segmentation to create a so (a spatial object datastructure) for further analysis. Researchers are encouraged to use their own preferred segmentation methods. For this tutorial, we use StarDist, which works well for many datasets. Here we use mouse brain data from 10x as example:

Lite version

• Soft Segmentation Tutorial (Lite version)

Full version (GPU needed)

• Soft Segmentation Tutorial (Full version)

Unrolling Example

• Unrolling Tutorial
• Unrolling (Mouse Brain Data)
• Unrolling (Mouse Small Intestine Data)

External reference: Nuclei segmentation (skip this section if you have already segmented your data with your preferred segmentation method)

• Nuclei Segmentation by StarDist