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+title = "anndata 0.13: layers meets X, zarr v3, and accessors"
+date = 2026-06-18T10:30:00+01:00
+description = "anndata 0.13 moves X into layers, makes zarr v3 the default, and introduces accessors for object-independent array references."
+author = "Ilan Gold"
+draft = false
++++
+
+We're thrilled to announce that `anndata` 0.13 is out now!
+We'll highlight some of the major changes here but be sure to check out [the changelog][] for the full list of changes, including breaking changes.
+
+# `X` is now a layer
+
+The biggest conceptual change in 0.13 is that the main expression matrix `X` is now stored as a layer, internally `layers[None]`.
+For most code this is invisible since you still access/read/write `adata.X` exactly as before.
+But treating `X` as just another layer moves us towards encouraging our users to be explicit about what `X` really is while lightening our code burden and unfiying behavior.
+Towards this end, our support for accessor objects (see below) will hopefully help make it easier for packages to declare what layers they expect to produce/consume.
+One **major breaking change** you will notice here is that anything relying on the keys of `layers` being all strings will now need to handle `None` as a key.
+
+## Copy-on-write for `X `
+As `X` is now a layer, writing into a view's `X` no longer mutates the parent `X`.
+This now matches how every other element (`obsm`, `var` etc.) already behaved:
+
+```python
+view = adata[:100]
+view.X = 0          # does NOT modify adata.X anymore, instead instantiates `view` as a fully in-memory `AnnData` object
+```
+
+If you were relying on the old propagating behavior, operate on the original object directly.
+
+# Zarr v3 by default
+
+We introduced support for the zarr v3 file-format as well as the v3 `zarr-python` package in 0.12.
+In 0.13 the file format v3 becomes the default, and support for `zarr-python<3` (i.e., the python package) is dropped entirely, however you can still opt-in to write v2 data.
+
+Concretely:
+
+- `anndata.settings.zarr_write_format` now defaults to `3` so all `write_zarr` calls in which the argument is a string file path will be v3
+- Automatic sharding is on by default (`anndata.settings.auto_shard_zarr_v3` targeting ~1GB uncompressed shards), so you get far fewer files per store with no manual tuning.
+
+If you want a refresher on what zarr v3 buys you, sharding to avoid file-system slowdowns, concurrent/parallel io, tips/tricks, and using rust-accelerated tooling like [zarrs-python][], the [zarr v3 guide][] and our [0.12 post][] cover it in depth.
+If `zarrs` is installed in your environment the bulk read/write functions i.e., `anndata.read_zarr` and `AnnData.write_zarr` will use it.
+
+# Accessors: object-independent array references
+
+0.13 introduces the new [`anndata.acc`][] module for referring to a vector or array *by location* without binding it to a specific object.
+
+The use cases for this feature abound: plotting functionality, validation, or arguments for things like "the `leiden` column" or "the first PCA component".
+Until now you'd pass around strings inlined into functions.
+Accessors now make these references first-class, fully supported objects that your package can export to users.
+
+You build references through the global `A` accessor:
+
+```python
+from anndata.acc import A
+
+A.X[:, "gene-3"]      # expression of one gene
+A.obsm["pca"][:, 0]   # first PCA component
+A.obs["louvain"]      # a cell-level annotation
+```
+
+These `AdRef` objects are independent of any AnnData instance.
+Furthermore you can inspect them (`.dims`, `.idx`, `.acc`), compare them for equality and use them as dictionary keys.
+To resolve a reference against an actual object i.e., index with it or test membership:
+
+```python
+ref = A.obs["louvain"]
+adata[ref]                          # indexes the anndata object, materializing an array
+A.varm["PCs"][:, 30] in adata       # answeres "does this reference exist here?" without loading the data
+```
+
+Accessors also work with `MuData` and are subclassable if you need custom behavior.
+
+If you are interested in schemas for `AnnData` please get in touch - we support [rudimentary serialization][] of accessors and have a schema for this output, but it can definitely be richer.
+Check it out and open an issue if you are interested!
+
+*— The scverse core team*
+
+[the changelog]: https://anndata.scverse.org/en/stable/release-notes/
+[zarrs-python]: https://zarrs-python.readthedocs.io/en/latest/
+[zarr v3 guide]: https://anndata.scverse.org/en/stable/tutorials/zarr-v3.html
+[0.12 post]: /blog/2025-anndata-012/
+[`anndata.acc`]: https://anndata.scverse.org/en/latest/accessors.html
+[rudimentary serialization]: https://anndata.scverse.org/en/latest/generated/anndata.acc.AdAcc.html#anndata.acc.AdAcc.to_json