cellxgene-census

1# CZ CELLxGENE Census
2 
3## Overview
4 
5The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first.
6 
7The Census includes:
8- **217+ million total cells** and **125+ million unique cells** in the 2025-11-08 stable LTS release
9- **1,845 datasets** in the 2025-11-08 stable LTS release
10- **Human, mouse, marmoset, rhesus macaque, and chimpanzee** data in the current schema
11- **Standardized metadata** (cell types, tissues, diseases, donors)
12- **Raw gene expression** matrices and source H5AD lookup/download helpers
13- **Pre-calculated summary counts, embeddings, and spatial data**
14- **Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools**
15 
16## When to Use This Skill
17 
18This skill should be used when:
19- Querying single-cell expression data by cell type, tissue, or disease
20- Exploring available single-cell datasets and metadata
21- Training machine learning models on single-cell data
22- Performing large-scale cross-dataset analyses
23- Integrating Census data with scanpy or other analysis frameworks
24- Computing statistics across millions of cells
25- Accessing pre-calculated embeddings or model predictions
26 
27## Installation and Setup
28 
29Install the Census API:
30```bash
31uv pip install "cellxgene-census==1.18.0"
32```
33…