zarr-tree v0.4.0

Highlights

v0.4.0 adds metadata-only structural validation to zarr-tree while preserving
its read-only inspection model.

Structural validation

• New --validate mode.
• PASS, WARN and ERROR findings, with a summary line.
• Text and JSON validation output (--validate --json).
• Exit status 2 when structural errors are found.
• Checks Zarr dimensions, OME-Zarr dataset paths and pyramids, HCS wells,
  SpatialData table regions, AnnData dimensions and SpatialData Parquet
  availability.
• Validation remains metadata-only: no image chunks, expression values or
  Parquet records are read.

Documentation and maintenance

• Reworked README as a project landing page.
• Added dedicated CLI, architecture, remote-store, Zarr, OME-Zarr and
  SpatialData documentation.
• Added CHANGELOG, CONTRIBUTING, SECURITY and GitHub contribution templates.

Compatibility

• Minimum supported Rust version is now 1.88.

Verification

• 112 tests (94 unit, 18 integration).
• CI checks formatting, Clippy, tests and the Rust 1.88 MSRV.
• Validation cross-checked against real OME-Zarr and SpatialData stores.

Known limitations

zarr-tree remains a metadata inspector, not an array reader or a full
format-conformance validator. It does not read image chunks, AnnData expression
values or Parquet records.

Full changelog: https://github.com/ronfinn/zarr-tree/blob/v0.4.0/CHANGELOG.md

zarr-tree v0.3.0

zarr-tree v0.3.0

This release expands zarr-tree from a local Zarr metadata inspector into a
remote and SpatialData-aware inspection tool.

Remote stores

• inspect Zarr stores directly on S3
• inspect HTTP/HTTPS stores using WebDAV-compatible listing
• traverse static HTTP stores using consolidated metadata
• support Zarr V2 .zmetadata
• support Zarr V3 inline consolidated_metadata

SpatialData

• inspect Parquet footer metadata for Points and Shapes
• report rows, columns, file counts and schemas without reading records
• summarize AnnData-backed Tables
• report observations, variables, X representation, obs/var columns and
  SpatialData region linkage
• distinguish unavailable Points payload metadata with parquet files: ?

Efficiency

• arrays remain leaves; chunk keys are not enumerated
• remote Parquet metadata uses bounded footer reads
• expression matrices are not read
• consolidated metadata can traverse an entire HTTP hierarchy with a single
  metadata document

Validation

Validated against real public data including:

• IDR OME-Zarr 0.3, 0.4 and 0.5
• OME-Zarr HCS
• Janelia COSEM
• Pangeo consolidated Zarr
• SpatialData Xenium
• SpatialData Visium
• SpatialData MERFISH
• SpatialData MIBI-TOF

The final public-data validation found no correctness bugs.

Scope

zarr-tree remains a read-only metadata inspection tool.

No chunk/pixel reads, Parquet row reads or expression-matrix reads are
performed.

zarr-tree v0.2.0

zarr-tree v0.2.0

This release expands real-world OME-Zarr and Zarr V3 support.

Highlights

• Correctly distinguishes inner chunks from shards for Zarr V3 arrays using
  sharding_indexed
• Adds a shards: metadata row for sharded arrays
• Adds shards to JSON output only when applicable
• Recognises OME-Zarr HCS plates
• Recognises OME-Zarr HCS wells
• Reports declared HCS row, column and well counts
• Preserves existing OME-Zarr image and SpatialData behaviour

Validation

Validated against real public metadata from:

• IDR OME-Zarr 0.3
• IDR OME-Zarr 0.4
• IDR OME-Zarr 0.5
• real HCS plate data
• scverse SpatialData MIBI-TOF
• scverse SpatialData Xenium

No incorrect metadata output was found in the final validation pass.

Scope

zarr-tree remains a local, metadata-only inspection CLI.

No binary assets and no crates.io publication yet.

zarr-tree v0.1.0

zarr-tree v0.1.0

First public release of zarr-tree, a small Rust CLI for exploring the
structure and metadata of local Zarr stores.

Highlights

• Inspect local Zarr V2 and V3 stores as a readable tree

• Recognise Zarr groups, arrays and unknown nodes

• Display array shape, chunk shape and dtype

• Recognise OME-Zarr image groups

• Display OME-NGFF axes and declared multiscale pyramid metadata

• Recognise SpatialData:

  • store roots
  • images
  • labels
  • points
  • shapes
  • tables

• Limit traversal with --depth

• Emit machine-readable output with --json

• Behave cleanly in Unix pipelines such as:

  zarr-tree store.zarr | head
  

Example

zarr-tree experiment.zarr

may produce:

experiment.zarr [group, SpatialData 0.2]
├── images [group]
│   └── morphology [group, OME-Zarr 0.5-dev-spatialdata, SpatialData image]
├── labels [group]
│   └── nuclei [group, OME-Zarr 0.5-dev-spatialdata, SpatialData labels]
├── points [group]
│   └── transcripts [group, SpatialData points]
├── shapes [group]
│   └── cell_boundaries [group, SpatialData shapes]
└── tables [group]
    └── table [group, SpatialData table]

Usage

Build from source:

git clone https://github.com/ronfinn/zarr-tree.git
cd zarr-tree
cargo build --release

Then run:

target/release/zarr-tree path/to/store.zarr

Useful options:

zarr-tree --depth 2 store.zarr
zarr-tree --json store.zarr
zarr-tree --json --depth 1 store.zarr

Scope

This release is intentionally metadata-only and local-filesystem-only.

It does not:

• read array chunks or pixel values
• decode Parquet or GeoParquet payloads
• interpret AnnData expression matrices
• access S3, HTTP or other remote object stores
• perform full OME-NGFF or SpatialData validation

OME-Zarr and SpatialData support is recognition and inspection rather than
full specification validation.

Quality

The v0.1.0 release was tagged from a clean build with:

• 37 unit tests
• 11 CLI integration tests
• cargo fmt --check
• cargo check
• cargo clippy --all-targets -- -D warnings
• cargo build --release

All checks passed.