cellxgene-census

Source: https://github.com/aipoch/medical-research-skills

When to Use

• Cross-tissue or cross-disease expression comparisons (e.g., macrophages across lung/liver/brain; COVID-19 vs control).
• Reference atlas lookups to contextualize findings from your own single-cell dataset (marker validation, expected expression patterns).
• Population-scale metadata exploration (what tissues/cell types/datasets exist; cell counts by cohort attributes).
• Large-scale expression statistics where results exceed RAM and require out-of-core iteration.
• Model training on curated atlas data (e.g., cell-type classifiers) using the experimental PyTorch integration.

Key Features

• Programmatic access to versioned CZ CELLxGENE Census data (human and mouse).
• Query cell (obs) metadata and gene (var) metadata with expressive filter syntax.
• Retrieve expression as AnnData for small/medium queries via get_anndata().
• Perform out-of-core expression access via SOMA axis_query() and chunked iteration.
• Optional experimental ML utilities (PyTorch dataloaders/datasets).
• Works well with scanpy workflows after loading AnnData.

Dependencies

• cellxgene-census (latest)
• tiledbsoma (latest; required for axis_query() workflows)
• pyarrow (latest; used for chunked table batches)
• anndata (latest; for get_anndata() results)
• scanpy (latest; optional, for downstream analysis)
• torch (latest; optional, for experimental ML integration)

Install:

uv pip install cellxgene-census

Optional (experimental ML helpers):

uv pip install cellxgene-census[experimental]

Example Usage

The following script is a complete, runnable example that:

1. opens a pinned Census version,
2. explores metadata,
3. loads a small AnnData slice, and
4. runs an out-of-core query to compute a simple statistic.

import numpy as np
import cellxgene_census
import tiledbsoma as soma

def main():
    # Pin a version for reproducibility (replace with a valid release if needed)
    census_version = "2023-07-25"

    with cellxgene_census.open_soma(census_version=census_version) as census:
        # 1) Explore summary info
        summary = census["census_info"]["summary"].read().concat().to_pandas()
        total_cells = int(summary["total_cell_count"].iloc[0])
        print(f"Census version: {census_version}")
        print(f"Total cells: {total_cells:,}")

        # 2) Explore obs metadata (always filter primary data unless you want duplicates)
        obs = cellxgene_census.get_obs(
            census,
            "homo_sapiens",
            value_filter="tissue_general == 'brain' and is_primary_data == True",
            column_names=["cell_type", "tissue_general", "disease", "donor_id"],
        )
        print(f"Brain (primary) cells returned (metadata only): {len(obs):,}")
        print("Top cell types:")
        print(obs["cell_type"].value_counts().head(10))

        # 3) Small/medium query -> AnnData in memory
        adata = cellxgene_census.get_anndata(
            census=census,
            organism="Homo sapiens",
            obs_value_filter=(
                "cell_type == 'T cell' and disease == 'COVID-19' and is_primary_data == True"
            ),
            var_value_filter="feature_name in ['CD4', 'CD8A', 'FOXP3']",
            obs_column_names=["cell_type", "tissue_general", "disease", "donor_id", "sex"],
        )
        print(adata)
        print("AnnData X shape:", adata.X.shape)

        # 4) Large-scale pattern -> out-of-core iteration with axis_query()
        # Example: compute mean of non-zero expression values for a few genes in brain.
        query = census["census_data"]["homo_sapiens"].axis_query(
            measurement_name="RNA",
            obs_query=soma.AxisQuery(
                value_filter="tissue_general == 'brain' and is_primary_data == True"
            ),
            var_query=soma.AxisQuery(
                value_filter="feature_name in ['FOXP2', 'TBR1', 'SATB2']"
            ),
        )

        n = 0
        s = 0.0
        for batch in query.X("raw").tables():
            # batch is a pyarrow.Table with at least: soma_data, soma_dim_0, soma_dim_1
            values = batch["soma_data"].to_numpy(zero_copy_only=False)
            n += values.size
            s += float(values.sum())

        mean_expr = s / n if n else np.nan
        print(f"Out-of-core mean expression (over returned entries): {mean_expr:.6g}")

if __name__ == "__main__":
    main()

Implementation Details

• Opening the Census

  • Use a context manager to ensure resources are released:
    • with cellxgene_census.open_soma(...) as census: ...
  • For reproducibility, set census_version="YYYY-MM-DD"; otherwise the latest stable release is used.

• Data model (high level)

  • Census data is stored in SOMA collections.
  • census["census_info"] provides summary tables (e.g., datasets, counts).
  • census["census_data"][organism] provides the experiment for an organism (e.g., homo_sapiens).

• Filtering semantics

  • obs_value_filter filters cells (obs); var_value_filter filters genes (var).
  • Combine predicates with and / or; use in [...] for multi-value membership.
  • Best practice: include is_primary_data == True to avoid double-counting cells that appear in multiple source datasets.

• Choosing an access pattern

  • Use get_anndata() when the result is expected to fit in memory (commonly < ~100k cells, depending on gene count and sparsity).
  • Use axis_query() + query.X("raw").tables() for out-of-core iteration and incremental statistics.

• Expression layers / matrices

  • Examples commonly use X("raw") to access raw expression.
  • Chunk iteration yields Arrow tables with:
    • soma_data: expression values
    • soma_dim_0: obs (cell) coordinates
    • soma_dim_1: var (gene) coordinates

• Optional ML integration

  • The cellxgene_census.experimental.ml utilities provide PyTorch-friendly datasets/dataloaders for training workflows, typically driven by the same obs/var filtering concepts used elsewhere.