InterSCellar

InterSCellar is a Python package for surface-Based cell neighborhood and interaction volume analysis in 3D spatial omics.

Installation

Install package:

pip install interscellar

Usage

Import:

import interscellar

3D Pipeline:

(1) Cell Neighbor Detection & Graph Construction

neighbors_3d, adata, conn = interscellar.find_cell_neighbors_3d(
    ome_zarr_path="data/segmentation.zarr",
    metadata_csv_path="data/cell_metadata.csv",
    max_distance_um=0.5,
    voxel_size_um=(0.56, 0.28, 0.28),
    n_jobs=4
)

(2) Interscellar Volume Computation

# Interscellar volumes
volumes_3d, adata, conn = interscellar.compute_interscellar_volumes_3d(
    ome_zarr_path="data/segmentation.zarr",
    neighbor_pairs_csv="results/neighbors_3d.csv",
    neighbor_db_path="/results/neighbor_graph.db",
    voxel_size_um=(0.56, 0.28, 0.28),
    max_distance_um=3.0,
    intracellular_threshold_um=1.0,
    n_jobs=4
)

# Cell-only volumes
cellonly_3d = interscellar.compute_cell_only_volumes_3d(
    ome_zarr_path="data/segmentation.zarr",
    interscellar_volumes_zarr="results/interscellar_volumes.zarr"
)

2D Pipeline:

(1) Cell Neighbor Detection & Graph Construction

neighbors_2d, adata, conn = interscellar.find_cell_neighbors_2d(
    polygon_json_path="data/cell_polygons.json",
    metadata_csv_path="data/cell_metadata.csv",
    max_distance_um=1.0,
    pixel_size_um=0.1085,
    n_jobs=4
)

Utilities:

Feature Extraction

feature-extract-3d \
  --segmentation-zarr "results/interscellar_volumes.zarr" \
  --raw-expression-zarr "data/raw_expression.zarr" \
  --output-csv "results/features_3d.csv"

Volume Visualization

# Full dataset (Napari)
visualize-all-3d \
  --cell-only-zarr "results/cell_only_volumes.zarr" \
  --interscellar-zarr "results/interscellar_volumes.zarr" \
  --cell-only-opacity 0.7 \
  --interscellar-opacity 0.9

# Single pair (Napari)
visualize-pair-3d \
  --pair-id 123 \
  --cell-only-zarr "results/cell_only_volumes.zarr" \
  --interscellar-zarr "results/interscellar_volumes.zarr" \
  --pair-opacity 0.6 \
  --cells-opacity 0.7