🚧 Version 0.3 Specification - Draft#

Last updated: October 29, 2026

Overview#

The Dynamic Cell Atlas (DCA) data resource provides 5D fluorescence microscopy datasets in a standardized format that makes them interchangeable for further processing.

The DCA standard aims to be optimized for handling 5D datasets (3D + time + channels). It also supports lower-dimensional data (2D + channels, 2D + time + channels, 3D + channels), but will not be optimized for it.

Use Cases#

The standard is designed to support multiple use cases:

  • Writing full arrays (data ingest)

  • Reading full arrays (data processing such as denoising, AI inference)

  • Reading partial arrays (visualization)

  • Reading with (pseudo-)random access (training AI models)

  • Copying full arrays (data management, backup)

While each use case might benefit from further optimization (e.g. chunk size), Zarr v3 chunking + sharding allows us to aim for a single array stored on disk that covers all use cases reasonably well.

Conformance#

Throughout this document, conformance requirements are expressed with descriptive assertions using RFC 2119 terminology:

  • MUST / REQUIRED / SHALL: Absolute requirement

  • MUST NOT / SHALL NOT: Absolute prohibition

  • SHOULD / RECOMMENDED: Strong recommendation

  • SHOULD NOT / NOT RECOMMENDED: Strong discouragement

  • MAY / OPTIONAL: Truly optional

Changes from v0.2#

  • Projections (new): layout and metadata for 2D projections of 3D images (maximum, mean or sum intensity, or a single plane), with a dca.projection block that records the method and the planes actually used, uniformly or per channel. The model is adapted from biahub’s project command. Its uniform form keeps the field names of the top-level mip attribute that v0.2-era projection stores carry. See Projections.

  • dca.version is "0.3".

  • image_data.processing_variant is an ordered list of processing steps, with a recommended step vocabulary, instead of a single string, and a new free-text image_data.processing_description holds the full processing text. These are the only changes to the experimental-metadata schema (schema/v0.3/dca_experimental_metadata.yaml).

  • The validator supports v0.3 with dca-validate --spec-version 0.3, including the cross-store projection checks and an opt-in --require-projection (see the v0.2 validator page for everything unchanged). The default spec version stays 0.2 until v0.3 is released.

Contents#

Previous Versions#