Cell Painting AnnData Validator¶
Validate the semantic correctness, metadata completeness, provenance and
basic AI readiness of Cell Painting datasets that are already stored as
AnnData (.h5ad) objects.
Beta status
Package version 0.2.0b1. Built-in schemas
(generic-cell-painting, jump-cp) are at 0.2.1. APIs and rule
codes are intended to be stable within this beta line, but the project
may still calibrate schemas and documentation before a final 0.2.0.
What this package does¶
- Reads an existing
.h5adfile (in-memory or backed) - Resolves canonical fields via versioned YAML schemas and declared aliases
- Detects or accepts a profile level (
single-cell,well,treatment) - Runs independent checks that return structured issues
- Renders console, JSON and HTML reports
What it does not do¶
- Convert CellProfiler, DeepProfiler, CytoTable or CSV profiles into AnnData
- Mutate or “fix” the input file
- Judge biological suitability, assay quality or scientific correctness of a phenotype
Quick links¶
| Install | Getting started → Installation |
| Five-minute path | Quickstart |
| CLI | CLI reference |
| Python | Python API |
| Rules | Rule catalogue |
| Pilots | Public-data pilots |
| Source | GitHub repository |