nuclear-spheroid-analysis

Two- and three-dimensional workflows for measuring nuclei in multicellular spheroids. The package connects object measurements with nucleus-to-spheroid assignment and inward/outward radial summaries.

Install

python -m pip install .

Example

from nuclear_spheroid_analysis import measure_spheroid_system

nuclei, spheroids = measure_spheroid_system(
    nuclear_image,
    nuclear_labels,
    spheroid_labels,
)

Add inward and outward radial bins using explicit pixel distances:

from nuclear_spheroid_analysis import analyze_radial_2d

radial, nuclei, spheroids = analyze_radial_2d(
    nuclei,
    spheroids,
    nuclear_labels,
    spheroid_labels,
    {
        "nbins-sph": 20,
        "maxdist-sph-shell": 400,
        "maxdist-sph-outward": 400,
    },
    {},
)

Persist each identity-preserving output for downstream analysis:

nuclei.to_csv("nuclear_features.csv", index=False)
spheroids.to_csv("spheroid_features.csv", index=False)
radial.to_csv("spheroid_radial_features.csv", index=False)

The resulting tables retain label identities, pixel coordinates, object sizes and spheroid membership. Radial analysis accepts explicit pixel distances and bin counts so the geometry can be tuned for each acquisition.