3D'omics ToolKit

Find, summarise, export and download 3D'omics catalogue records from the command line or Python.

Open source research software

A direct route to the 3D'omics catalogue

3dtk is the 3D'omics ToolKit: a Python package and command-line interface for querying the published 3D'omics catalogue. It uses a citable, checksum-verified SQLite release from Zenodo, so researchers can work with the data without credentials or a running server.

Install the 3dtk distribution, then use py3dtk in Python.

pip install 3dtk
3dtk database sync
3dtk microsamples query --experiment-id G --sex female --columns context

View the source on GitHub Read the documentation

Built for practical data access

Use one consistent interface across the 3D'omics data hierarchy: experiments, specimens, macro- and microsamples, cryosections, genomes and count matrices.

Query and summarise

Filter records, discover available fields and values, and produce quick statistics across the catalogue.

Export analysis-ready data

Rebuild dense count matrices and pair them with aligned spatial coordinates for downstream analysis.

Fetch sequencing files

Resolve catalogue accessions and download sequencing data with integrity checks and an auditable manifest.