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anndata - Annotated data#

anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.

anndata is part of the scverse project (website, governance) and is fiscally sponsored by NumFOCUS. Please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.


If you use anndata in your work, please cite the anndata pre-print as follows:

anndata: Annotated data

Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf

bioRxiv 2021 Dec 19. doi: 10.1101/2021.12.16.473007.

You can cite the scverse publication as follows:

The scverse project provides a computational ecosystem for single-cell omics data analysis

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis

Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.

Latest additions#

Version 0.11#

0.11.0 the future#






  • Removed deprecated modules anndata.core and anndata.readwrite #1197 @ivirshup

Version 0.10#

0.10.4 the future#


  • Only try to use…) in actually supported Pandas ≥2.1 #1226 @flying-sheep

  • AnnData.__sizeof__() support for backed datasets #1230 @Neah-Ko

  • adata[:, []] now returns an AnnData object empty on the appropriate dimensions instead of erroring #1243 @ilan-gold



0.10.3 2023-10-31#


  • Prevent pandas from causing infinite recursion when setting a slice of a categorical column #1211 @flying-sheep


  • Stop showing “Support for Awkward Arrays is currently experimental” warnings when reading, concatenating, slicing, or transposing AnnData objects #1182 @flying-sheep

Other updates

0.10.2 2023-10-11#



0.10.1 2023-10-08#


  • Fix ad.concat erroring when concatenating a categorical and object column #1171 @ivirshup

0.10.0 2023-10-06#


GPU Support

Out of core

Improved errors and warnings

  • Improved error messages when combining dataframes with duplicated column names #1029 @ivirshup

  • Improved warnings when modifying views of AlingedMappings #1016 @flying-sheep @ivirshup

  • AnnDataReadErrors have been removed. The original error is now thrown with additional information in a note #1055 @ivirshup


Breaking changes

Other updates


Bug fixes

See Release notes for more.


Muon paper published 2022-02-02#

Muon has been published in Genome Biology [^cite_bredikhin22]. Muon is a framework for multimodal data built on top of AnnData.

Check out Muon and its datastructure MuData.

COVID-19 datasets distributed as h5ad 2020-04-01#

In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s h5ad files: