nichemap 0.1.1

A spatial grid-based toolkit for niche identification and cell-type neighborhood analysis in spatial transcriptomics

NicheMap

NicheMap is a Python toolkit for spatial niche analysis in Xenium and other coordinate-resolved spatial transcriptomics data.

NicheMap supports two complementary workflows:

• spatial niche identification from marker-gene signature scores
• cell-type neighborhood analysis around annotated spatial structures

Installation

pip install nichemap

For local development from source:

git clone https://github.com/yihe-csu/NicheMap.git
cd NicheMap
pip install -e .

Quick Start

Spatial niche identification

from pathlib import Path

import nichemap as nm

adata = nm.preprocess.load_xenium_data(
    base_dir=r"F:\spatial_data_lung\SSc_1_1_2_raw",
    anno_file=r"F:\spatial_data_lung\ssc112_annotation_map.csv",
)

model = nm.NicheMap(
    adata=adata,
    score_id="ECM_score",
    sample_prefix="SSc_1_1_2",
    out_dir=Path("outputs/ECM_score"),
)

final_adata = model.run(
    gene_list_csv=r"F:\spatial_data_lung\marker_genes\ECM-gene.csv",
    bins=300,
    peak_intensity=1.5,
    exp_intensity=1.0,
)

Cell-type neighborhood analysis

import scanpy as sc
import nichemap.neighborhood as nh

adata = sc.read_h5ad("data/SSc_1_1_2_tutorial.h5ad")

results = nh.run_cell_type_neighborhood_analysis(
    adata=adata,
    target_regions=["Airway_wall"],
    hops=[1, 2, 3],
    structure_col="structure_label",
    cell_type_col="cell_type",
    output_dir="outputs/neighborhood",
    selected_cell_types=None,
    make_plots=True,
)

Documentation and Tutorials

• GitHub repository: https://github.com/yihe-csu/NicheMap
• Online tutorials: https://nichemap-tutorials.readthedocs.io/en/latest/
• Usage guide: https://github.com/yihe-csu/NicheMap/blob/main/How%20to%20use%20NicheMap.md
• Tutorials: https://github.com/yihe-csu/NicheMap/tree/main/Tutorials

Citation

If you use NicheMap in your work, please cite:

He, Y. et al. NicheMap: a spatial grid-based pipeline for niche identification
in spatial transcriptomics. (Manuscript in preparation)

License

NicheMap is released under the MIT License.